Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000535.7(PMS2):c.1144+1G>A

CA009232

162508 (ClinVar)

Gene: PMS2
Condition: Lynch syndrome 1
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 399b7542-9fcc-474f-9408-99aa3c9f8663
Approved on: 2024-09-19
Published on: 2024-10-11

HGVS expressions

NM_000535.7:c.1144+1G>A
NM_000535.7(PMS2):c.1144+1G>A
NC_000007.14:g.5989799C>T
CM000669.2:g.5989799C>T
NC_000007.13:g.6029430C>T
CM000669.1:g.6029430C>T
NC_000007.12:g.5995956C>T
NG_008466.1:g.24308G>A
ENST00000699814.2:c.*540+1G>A
ENST00000699840.2:c.1141+1G>A
ENST00000699930.2:c.1036+1G>A
ENST00000406569.8:c.1144+1G>A
ENST00000644110.2:c.*738+1G>A
ENST00000699752.1:c.988+2174G>A
ENST00000699753.1:c.*565+1G>A
ENST00000699754.1:c.946+1G>A
ENST00000699755.1:c.*543+1G>A
ENST00000699756.1:c.*731+1G>A
ENST00000699757.1:c.*401+1G>A
ENST00000699758.1:c.*401+1G>A
ENST00000699759.1:n.1998+1G>A
ENST00000699760.1:c.826+1G>A
ENST00000699761.1:c.739+1G>A
ENST00000699762.1:c.571+1G>A
ENST00000699763.1:c.*234+1G>A
ENST00000699764.1:c.1144+1G>A
ENST00000699765.1:c.*240+1G>A
ENST00000699766.1:c.1144+1G>A
ENST00000699767.1:c.1144+1G>A
ENST00000699768.1:c.1144+1G>A
ENST00000699811.1:c.739+1G>A
ENST00000699813.1:n.1257+1G>A
ENST00000699814.1:c.767+1G>A
ENST00000699815.1:c.*636+1G>A
ENST00000699816.1:c.739+1G>A
ENST00000699817.1:c.*738+1G>A
ENST00000699818.1:c.739+1G>A
ENST00000699819.1:c.*301+1G>A
ENST00000699820.1:c.1144+1G>A
ENST00000699821.1:c.739+1G>A
ENST00000699822.1:c.*596+1G>A
ENST00000699823.1:c.739+1G>A
ENST00000699824.1:c.*647+1G>A
ENST00000699825.1:c.583+2174G>A
ENST00000699826.1:c.*543+1G>A
ENST00000699827.1:c.976+1G>A
ENST00000699828.1:c.*234+1G>A
ENST00000699829.1:c.*645+1G>A
ENST00000699830.1:c.*543+1G>A
ENST00000699833.1:n.2916+1G>A
ENST00000699837.1:c.739+1G>A
ENST00000699838.1:c.*1044+1G>A
ENST00000699839.1:c.1330+1G>A
ENST00000699840.1:c.1141+1G>A
ENST00000699916.1:c.*401+1G>A
ENST00000699917.1:c.*593+1G>A
ENST00000699918.1:c.*645+1G>A
ENST00000699919.1:c.*731+1G>A
ENST00000699920.1:c.*780+1G>A
ENST00000699928.1:c.988+2174G>A
ENST00000699929.1:c.*445+1G>A
ENST00000699930.1:c.1036+1G>A
ENST00000699931.1:n.2572+1G>A
ENST00000699932.1:c.*362+1G>A
ENST00000699933.1:n.1125G>A
ENST00000699951.1:c.*240+1G>A
ENST00000699952.1:c.803+7527G>A
ENST00000699953.1:c.*251+1G>A
ENST00000699954.1:c.*445+1G>A
ENST00000265849.12:c.1144+1G>A
ENST00000642292.1:c.739+1G>A
ENST00000642456.1:c.739+1G>A
ENST00000643595.1:c.*543+1G>A
ENST00000644110.1:c.826+1G>A
ENST00000265849.11:c.1144+1G>A
ENST00000382321.5:c.804-6808G>A
ENST00000406569.7:n.1144+1G>A
ENST00000441476.6:c.826+1G>A
ENST00000469652.1:n.63-6894G>A
NM_000535.5:c.1144+1G>A
NR_003085.2:n.1226+1G>A
NM_000535.6:c.1144+1G>A
NM_001322003.1:c.739+1G>A
NM_001322004.1:c.739+1G>A
NM_001322005.1:c.739+1G>A
NM_001322006.1:c.988+2174G>A
NM_001322007.1:c.826+1G>A
NM_001322008.1:c.826+1G>A
NM_001322009.1:c.739+1G>A
NM_001322010.1:c.583+2174G>A
NM_001322011.1:c.211+1G>A
NM_001322012.1:c.211+1G>A
NM_001322013.1:c.571+1G>A
NM_001322014.1:c.1144+1G>A
NM_001322015.1:c.835+1G>A
NR_136154.1:n.1231+1G>A
NM_001322003.2:c.739+1G>A
NM_001322004.2:c.739+1G>A
NM_001322005.2:c.739+1G>A
NM_001322006.2:c.988+2174G>A
NM_001322008.2:c.826+1G>A
NM_001322009.2:c.739+1G>A
NM_001322010.2:c.583+2174G>A
NM_001322011.2:c.211+1G>A
NM_001322012.2:c.211+1G>A
NM_001322013.2:c.571+1G>A
NM_001322014.2:c.1144+1G>A
NM_001322015.2:c.835+1G>A
NM_001322007.2:c.826+1G>A
More

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PVS1_Strong PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP
The NM_000535.7:c.1144+1G>A p.(?) variant in PMS2 occurs within the canonical splice donor site (+1) of intron 10. It is predicted to result in an in-frame exon skipping and the altered region is critical to protein function (PVS1_Strong). The variant was detected in one CRC/Endometrial MSI-H tumour using a standard panel of 5-10 markers and/or loss of MMR protein expression consistent with the variant location (PP4). This variant is extremely rare (2 in 267958 alleles) in gnomAD using the non cancer dataset and also the gnomAD v4.1 Grpmax AF is 6.856e-7 (PM2_Supporting). In summary, this variant meets the criteria to be classified as likely pathogenic for Lynch-Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/ Polyposis VCEP: PVS1_STR, PM2_SUP, PP4 (VCEP specifications version 1)
Met criteria codes
PM2_Supporting
This variant is extremely rare (2 in 267958 alleles) in gnomAD using the non cancer dataset (PM2_Supporting) (Update: gnomAD v4.1 Grpmax AF = 6.856e-7)
PVS1_Strong
The variant occurs within the canonical splice donor site (+1) of intron 10. It is predicted to result in an in-frame exon skipping and the altered region is critical to protein function (PVS1_Strong).
PP4
The variant was detected in one CRC/Endometrial MSI-H tumour using a standard panel of 5-10 markers and/or loss of MMR protein expression consistent with the variant location (PP4).
Curation History
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