ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1868_1876delinsTA (p.Ala623fs)
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_000251.3(MSH2):c.1868_1876delinsTA (p.Ala623fs)
Variation ID: 2673366 Accession: VCV002673366.1
- Type and length
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Indel, 9 bp
- Location
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Cytogenetic: 2p21 2: 47475133-47475141 (GRCh38) [ NCBI UCSC ] 2: 47702272-47702280 (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 25, 2023 Dec 24, 2023 Aug 4, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.1868_1876delinsTA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Ala623fs frameshift NM_001258281.1:c.1670_1678delinsTA NP_001245210.1:p.Ala557fs frameshift NM_001406631.1:c.1868_1876delinsTA NP_001393560.1:p.Ala623fs frameshift NM_001406632.1:c.1868_1876delinsTA NP_001393561.1:p.Ala623fs frameshift NM_001406633.1:c.1868_1876delinsTA NP_001393562.1:p.Ala623fs frameshift NM_001406634.1:c.1868_1876delinsTA NP_001393563.1:p.Ala623fs frameshift NM_001406635.1:c.1868_1876delinsTA NP_001393564.1:p.Ala623fs frameshift NM_001406636.1:c.1835_1843delinsTA NP_001393565.1:p.Ala612fs frameshift NM_001406637.1:c.1868_1876delinsTA NP_001393566.1:p.Ala623fs frameshift NM_001406638.1:c.1907_1915delinsTA NP_001393567.1:p.Ala636fs frameshift NM_001406639.1:c.1868_1876delinsTA NP_001393568.1:p.Ala623fs frameshift NM_001406640.1:c.1868_1876delinsTA NP_001393569.1:p.Ala623fs frameshift NM_001406641.1:c.1868_1876delinsTA NP_001393570.1:p.Ala623fs frameshift NM_001406642.1:c.1868_1876delinsTA NP_001393571.1:p.Ala623fs frameshift NM_001406643.1:c.1868_1876delinsTA NP_001393572.1:p.Ala623fs frameshift NM_001406644.1:c.1868_1876delinsTA NP_001393573.1:p.Ala623fs frameshift NM_001406645.1:c.1868_1876delinsTA NP_001393574.1:p.Ala623fs frameshift NM_001406646.1:c.1868_1876delinsTA NP_001393575.1:p.Ala623fs frameshift NM_001406647.1:c.1718_1726delinsTA NP_001393576.1:p.Ala573fs frameshift NM_001406648.1:c.1868_1876delinsTA NP_001393577.1:p.Ala623fs frameshift NM_001406649.1:c.1718_1726delinsTA NP_001393578.1:p.Ala573fs frameshift NM_001406650.1:c.1718_1726delinsTA NP_001393579.1:p.Ala573fs frameshift NM_001406651.1:c.1718_1726delinsTA NP_001393580.1:p.Ala573fs frameshift NM_001406652.1:c.1718_1726delinsTA NP_001393581.1:p.Ala573fs frameshift NM_001406653.1:c.1808_1816delinsTA NP_001393582.1:p.Ala603fs frameshift NM_001406654.1:c.1448_1456delinsTA NP_001393583.1:p.Ala483fs frameshift NM_001406655.1:c.1868_1876delinsTA NP_001393584.1:p.Ala623fs frameshift NM_001406656.1:c.971_979delinsTA NP_001393585.1:p.Ala324fs frameshift NM_001406657.1:c.*78_*86delinsTA 3 prime UTR NM_001406658.1:c.512_520delinsTA NP_001393587.1:p.Ala171fs frameshift NM_001406659.1:c.512_520delinsTA NP_001393588.1:p.Ala171fs frameshift NM_001406660.1:c.512_520delinsTA NP_001393589.1:p.Ala171fs frameshift NM_001406661.1:c.512_520delinsTA NP_001393590.1:p.Ala171fs frameshift NM_001406662.1:c.512_520delinsTA NP_001393591.1:p.Ala171fs frameshift NM_001406669.1:c.512_520delinsTA NP_001393598.1:p.Ala171fs frameshift NM_001406674.1:c.1868_1876delinsTA NP_001393603.1:p.Ala623fs frameshift NR_176230.1:n.1904_1912delinsTA non-coding transcript variant NR_176231.1:n.1904_1912delinsTA non-coding transcript variant NR_176232.1:n.1904_1912delinsTA non-coding transcript variant NR_176233.1:n.1746_1754delinsTA non-coding transcript variant NR_176234.1:n.1904_1912delinsTA non-coding transcript variant NR_176235.1:n.1904_1912delinsTA non-coding transcript variant NR_176236.1:n.1904_1912delinsTA non-coding transcript variant NR_176237.1:n.1904_1912delinsTA non-coding transcript variant NR_176238.1:n.2037_2045delinsTA non-coding transcript variant NR_176239.1:n.1904_1912delinsTA non-coding transcript variant NR_176240.1:n.1904_1912delinsTA non-coding transcript variant NR_176241.1:n.1904_1912delinsTA non-coding transcript variant NR_176242.1:n.1904_1912delinsTA non-coding transcript variant NR_176243.1:n.1754_1762delinsTA non-coding transcript variant NR_176244.1:n.1904_1912delinsTA non-coding transcript variant NR_176245.1:n.1904_1912delinsTA non-coding transcript variant NR_176246.1:n.1904_1912delinsTA non-coding transcript variant NR_176247.1:n.1904_1912delinsTA non-coding transcript variant NR_176248.1:n.1904_1912delinsTA non-coding transcript variant NR_176249.1:n.2134_2142delinsTA non-coding transcript variant NR_176250.1:n.1644_1652delinsTA non-coding transcript variant NC_000002.12:g.47475133_47475141delinsTA NC_000002.11:g.47702272_47702280delinsTA NG_007110.2:g.77010_77018delinsTA LRG_218:g.77010_77018delinsTA LRG_218t1:c.1868_1876delCCATTTTGGinsTA LRG_218p1:p.Ala623Valfs - Protein change
- A171fs, A324fs, A483fs, A557fs, A573fs, A603fs, A612fs, A623fs, A636fs
- Other names
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- Canonical SPDI
- NC_000002.12:47475132:CCATTTTGG:TA
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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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- 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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MSH2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
7401 | 7563 |
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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Pathogenic (1) |
criteria provided, single submitter
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Aug 4, 2023 | RCV003450089.1 |
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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Pathogenic
(Aug 04, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004187031.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Jun 10, 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.