ClinVar Genomic variation as it relates to human health
NM_000520.6(HEXA):c.672+30T>G
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_000520.6(HEXA):c.672+30T>G
Variation ID: 256351 Accession: VCV000256351.30
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q23 15: 72351103 (GRCh38) [ NCBI UCSC ] 15: 72643444 (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 Oct 3, 2016 Apr 15, 2024 Feb 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000520.6:c.672+30T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001318825.2:c.705+30T>G intron variant NC_000015.10:g.72351103A>C NC_000015.9:g.72643444A>C NG_009017.2:g.30077T>G - Protein change
- Other names
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- Canonical SPDI
- NC_000015.10:72351102:A: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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0.01438 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 0.01438
The Genome Aggregation Database (gnomAD) 0.01494
Trans-Omics for Precision Medicine (TOPMed) 0.01498
1000 Genomes Project 30x 0.01515
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01909
The Genome Aggregation Database (gnomAD), exomes 0.01909
Exome Aggregation Consortium (ExAC) 0.01969
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
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
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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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HEXA | - | - |
GRCh38 GRCh37 |
1127 | 1161 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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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Benign (5) |
criteria provided, multiple submitters, no conflicts
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Feb 11, 2019 | RCV000250930.19 | |
Benign (5) |
criteria provided, multiple submitters, no conflicts
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Feb 1, 2024 | RCV000416442.12 | |
Likely benign (2) |
criteria provided, single submitter
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Apr 19, 2019 | RCV000675468.6 |
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
Help
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
Help
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
Help
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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Benign
(-)
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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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PreventionGenetics, part of Exact Sciences
Accession: SCV000304642.1
First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016 |
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Benign
(Mar 28, 2016)
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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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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000539284.1
First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: frequency. OB 12/23/15: 4.6% freq in South Asian chr (less)
Method: Genome/Exome Filtration
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Benign
(Dec 30, 2017)
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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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Eurofins Ntd Llc (ga)
Accession: SCV000859033.1
First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016 |
Number of individuals with the variant: 1
Sex: mixed
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Benign
(Feb 11, 2019)
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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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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156690.1
First in ClinVar: Feb 10, 2020 Last updated: Feb 10, 2020 |
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Benign
(-)
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criteria provided, single submitter
Method: research
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Tay-Sachs disease
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001435134.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Comment:
The c.672+30T>G variant in HEXA has been identified in at least 1 Tay-Sachs disease carrier (PMID: 7717398), and has been identified in >4% of South … (more)
The c.672+30T>G variant in HEXA has been identified in at least 1 Tay-Sachs disease carrier (PMID: 7717398), and has been identified in >4% of South Asian chromosomes and 43 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for Tay-Sachs disease. (less)
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Benign
(Jun 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Tay-Sachs disease
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001737377.1
First in ClinVar: Jun 19, 2021 Last updated: Jun 19, 2021 |
Sex: mixed
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Likely benign
(Apr 19, 2019)
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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: SCV001786210.1
First in ClinVar: Aug 14, 2021 Last updated: Aug 14, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 9150157, 28492530, 22723944, 27535533, 27884173, 7717398)
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Benign
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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Tay-Sachs disease
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001731225.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 28, 2024 |
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Benign
(May 04, 2023)
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criteria provided, single submitter
Method: clinical testing
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Tay-Sachs disease
Affected status: yes
Allele origin:
germline
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Molecular Genetics, Royal Melbourne Hospital
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004812379.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Comment:
South Asian population allele frequency is 4.368% (rs117160567, 1395/30540 alleles, 49 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.3.2, … (more)
South Asian population allele frequency is 4.368% (rs117160567, 1395/30540 alleles, 49 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.3.2, this variant is classified as BENIGN. Following criteria are met: BA1 (less)
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Pathogenic
(Mar 22, 2011)
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no assertion criteria provided
Method: research
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Tay-Sachs disease
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV000494214.1
First in ClinVar: Feb 04, 2017 Last updated: Feb 04, 2017 |
Age: 0-9 years
Sex: male
Ethnicity/Population group: Indian
Geographic origin: India
Tissue: Blood
Method: Polymerase Chain Reaction followed by bi-directional Sanger sequencing was performed covering all exons and exon-intron boundaries of the HEXA gene.
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Benign
(Apr 05, 2017)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801157.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
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: SCV001553064.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
Comment:
The HEXA c.705+30T>G variant was not identified in the ClinVar, Cosmic, MutDB or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs117160567) and … (more)
The HEXA c.705+30T>G variant was not identified in the ClinVar, Cosmic, MutDB or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs117160567) and in control databases in 5209 of 282340 chromosomes (93 homozygous) at a frequency of 0.018449 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: South Asian in 1395 of 30540 chromosomes (freq: 0.04568), European (non-Finnish) in 2954 of 128924 chromosomes (freq: 0.02291), Ashkenazi Jewish in 197 of 10352 chromosomes (freq: 0.01903), Other in 114 of 7212 chromosomes (freq: 0.01581), European (Finnish) in 194 of 25090 chromosomes (freq: 0.007732), Latino in 246 of 35372 chromosomes (freq: 0.006955), African in 105 of 24924 chromosomes (freq: 0.004213) and East Asian in 4 of 19926 chromosomes (freq: 0.000201). This variant was identified in an unaffected carrier with another disease-causing mutation for Tay-Sachs disease, suggesting that this variant is not associated with disease (Triggs-Rainer_1995_PMID:7717398). The c.705+30T>G variant occurs outside the splicing consensus sequence and is not predicted to have an impact on splicing by 4 of 4 in silico splicing softwares (SpliceSiteFinder-Like, MaxEntScan, NNSplice, GeneSplicer). In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. (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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Identification of novel mutations in HEXA gene in children affected with Tay Sachs disease from India. | Mistri M | PloS one | 2012 | PMID: 22723944 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HEXA | - | - | - | - |
Text-mined citations for rs117160567 ...
HelpRecord last updated Apr 15, 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.