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NM_000535.7(PMS2):c.988+4A>G

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 30, 2021)
Last evaluated:
May 21, 2021
Accession:
VCV000385124.7
Variation ID:
385124
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.988+4A>G

Allele ID
369838
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5991969 (GRCh38) GRCh38 UCSC
7: 6031600 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.22138A>G
LRG_161t1:c.988+4A>G
NC_000007.14:g.5991969T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:5991968:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA052770
dbSNP: rs763959308
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Nov 2, 2020 RCV000555625.6
Likely benign 1 criteria provided, single submitter May 21, 2021 RCV001720229.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 19, 2019 RCV000579979.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PMS2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3086 3151

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 22, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686264.1
Submitted: (Oct 26, 2017)
Evidence details
Uncertain significance
(Nov 02, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000625712.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change falls in intron 9 of the PMS2 gene. It does not directly change the encoded amino acid sequence of the PMS2 protein, … (more)
Likely benign
(May 21, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000526277.5
Submitted: (Sep 30, 2021)
Evidence details
Uncertain significance
(Aug 19, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV001181266.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The c.988+4A>G intronic variant results from an A to G substitution 4 nucleotides after coding exon 9 in the PMS2 gene. This nucleotide position is … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs763959308...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021