ClinVar Genomic variation as it relates to human health
NM_007194.4(CHEK2):c.1076A>G (p.Glu359Gly)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_007194.4(CHEK2):c.1076A>G (p.Glu359Gly)
Variation ID: 233678 Accession: VCV000233678.29
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 22q12.1 22: 28696920 (GRCh38) [ NCBI UCSC ] 22: 29092908 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 19, 2017 Sep 16, 2024 Sep 9, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_007194.4:c.1076A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_009125.1:p.Glu359Gly missense NM_001005735.2:c.1205A>G NP_001005735.1:p.Glu402Gly missense NM_001257387.2:c.413A>G NP_001244316.1:p.Glu138Gly missense NM_001349956.2:c.875A>G NP_001336885.1:p.Glu292Gly missense NM_145862.2:c.1009-1047A>G intron variant NC_000022.11:g.28696920T>C NC_000022.10:g.29092908T>C NG_008150.2:g.49947A>G LRG_302:g.49947A>G LRG_302t1:c.1076A>G LRG_302p1:p.Glu359Gly - Protein change
- E359G, E402G, E292G, E138G
- Other names
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- Canonical SPDI
- NC_000022.11:28696919:T:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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CHEK2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
4053 | 4109 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Oct 31, 2023 | RCV000222729.13 | |
Uncertain significance (2) |
criteria provided, single submitter
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Jun 9, 2024 | RCV000482650.6 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Jan 20, 2024 | RCV000635710.13 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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May 13, 2024 | RCV001818540.5 | |
Uncertain significance (1) |
criteria provided, single submitter
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Sep 9, 2024 | RCV004701296.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Oct 31, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000278103.7
First in ClinVar: May 29, 2016 Last updated: May 01, 2024 |
Comment:
The p.E359G variant (also known as c.1076A>G), located in coding exon 9 of the CHEK2 gene, results from an A to G substitution at nucleotide … (more)
The p.E359G variant (also known as c.1076A>G), located in coding exon 9 of the CHEK2 gene, results from an A to G substitution at nucleotide position 1076. The glutamic acid at codon 359 is replaced by glycine, an amino acid with similar properties. This alteration was identified in a cohort of 1260 individuals undergoing panel testing for Lynch syndrome due to having a diagnosis of a Lynch-associated cancer and/or polyps (Yurgelun MB et al. Gastroenterology, 2015 Sep;149:604-13.e20). This alteration has also been reported in at least one breast cancer patient in a study of 13087 breast cancer cases and 5488 control individuals in the UK (Decker B et al. J Med Genet, 2017 11;54:732-741).This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
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Uncertain significance
(Jun 09, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000566258.6
First in ClinVar: Apr 29, 2017 Last updated: Jul 23, 2024 |
Comment:
Observed in individuals with breast cancer or a Lynch syndrome-related cancer and/or polyps (PMID: 25980754, 37449874); Published functional studies demonstrate KAP1 phosphorylation and CHK2 auto-phosphorylation … (more)
Observed in individuals with breast cancer or a Lynch syndrome-related cancer and/or polyps (PMID: 25980754, 37449874); Published functional studies demonstrate KAP1 phosphorylation and CHK2 auto-phosphorylation comparable to wild-type (PMID: 37449874); RNA studies demonstrate aberrant splicing resulting in both in-frame and out-of-frame transcripts (PMID: 38332730); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25980754, 28576879, 28779002, 30262796, 22419737, 19782031, 33471991, 35451682, 37449874, 38332730) (less)
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Uncertain significance
(Nov 29, 2021)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: no
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV002065798.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
Comment:
DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.1076A>G, in exon 10 that results in an amino acid change, p.Glu359Gly. This sequence … (more)
DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.1076A>G, in exon 10 that results in an amino acid change, p.Glu359Gly. This sequence change has been described in the gnomAD database in two individuals which corresponds to a population frequency of 0.0018 % (dbSNP rs760449049). The p.Glu359Gly change affects a moderately conserved amino acid residue located in a domain of the CHEK2 protein that is known to be functional. The p.Glu359Gly substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change does not appear to have been previously described in individuals with CHEK2-related disorders. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Glu359Gly change remains unknown at this time. (less)
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Uncertain significance
(Oct 10, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV000689628.5
First in ClinVar: Feb 19, 2018 Last updated: Feb 14, 2024 |
Comment:
This missense variant replaces glutamic acid with glycine at codon 359 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein … (more)
This missense variant replaces glutamic acid with glycine at codon 359 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual suspected of having Lynch syndrome (PMID: 25980754) and in two unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID CHEK2_000369). This variant has been identified in 2/251266 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. (less)
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Uncertain significance
(Jan 10, 2024)
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criteria provided, single submitter
Method: clinical testing
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Familial cancer of breast
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000757131.8
First in ClinVar: May 28, 2018 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 359 of the CHEK2 protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 359 of the CHEK2 protein (p.Glu359Gly). This variant is present in population databases (rs760449049, gnomAD 0.002%). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 25980754). ClinVar contains an entry for this variant (Variation ID: 233678). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
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Uncertain significance
(Jan 20, 2024)
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criteria provided, single submitter
Method: clinical testing
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Familial cancer of breast
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004217610.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Uncertain significance
(May 13, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV005184788.1
First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024 |
Comment:
Variant summary: CHEK2 c.1076A>G (p.Glu359Gly) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Three … (more)
Variant summary: CHEK2 c.1076A>G (p.Glu359Gly) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251266 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1076A>G has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome as well as healthy controls (e.g., Yurgelun_2015, Decker_2017, Stolarova_2023). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant on kinase activity (e.g., Stolarova_2023). The following publications have been ascertained in the context of this evaluation (PMID: 37449874, 25980754, 28779002). ClinVar contains an entry for this variant (Variation ID: 233678). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. (less)
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Uncertain significance
(Sep 09, 2024)
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criteria provided, single submitter
Method: clinical testing
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Li-Fraumeni syndrome 2
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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KCCC/NGS Laboratory, Kuwait Cancer Control Center
Accession: SCV005201092.1
First in ClinVar: Sep 16, 2024 Last updated: Sep 16, 2024 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and nonpolar, at codon 359 of the CHEK2 protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and nonpolar, at codon 359 of the CHEK2 protein (p.Glu359Gly)This amino acid position is poorly conserved (PhyloP=3.45) . This variant is present in population databases (rs760449049, gnomAD 0.002%). This missense change has been observed in individual(s) with Lynch syndrome PMID: 25980754, 28576879, 28779002, 30262796, 22419737, 19782031, 33471991, 35451682, 37449874, 38332730). ClinVar contains an entry for this variant (Variation ID: 233678). In addition, this alteration is predicted to be tolerated by in silico analysis. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.Pathogenic/likely pathogenic mutations in the CHEK2 gene cause susceptibility to breast cancer (OMIM# 114480). (less)
Age: 50-59 years
Sex: female
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Uncertain significance
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001553264.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
Comment:
The CHEK2 p.Glu359Gly variant was identified in 1 of 2520 proband chromosomes (frequency: 0.0004) from individuals or families with Lynch syndrome (Yurgelun 2015). The variant … (more)
The CHEK2 p.Glu359Gly variant was identified in 1 of 2520 proband chromosomes (frequency: 0.0004) from individuals or families with Lynch syndrome (Yurgelun 2015). The variant was also identified in dbSNP (ID: rs760449049) as "With Uncertain significance allele" and ClinVar (classified as uncertain significance by Invitae, GeneDx, Ambry Genetics, and Color). The variant was not identified in the Cosmic, MutDB, Zhejiang University database, the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The p.Glu359 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. | Stolarova L | Clinical cancer research : an official journal of the American Association for Cancer Research | 2023 | PMID: 37449874 |
Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. | Breast Cancer Association Consortium | The New England journal of medicine | 2021 | PMID: 33471991 |
Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. | Decker B | Journal of medical genetics | 2017 | PMID: 28779002 |
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. | Yurgelun MB | Gastroenterology | 2015 | PMID: 25980754 |
Text-mined citations for rs760449049 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.