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_000249.4(MLH1):c.2040C>T (p.Cys680=)

CA008297

90010 (ClinVar)

Gene: MLH1
Condition: Lynch syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 70a1d4a4-791a-494a-a70e-fc4c558d31d5
Approved on: 2024-09-19
Published on: 2024-10-11

HGVS expressions

NM_000249.4:c.2040C>T
NM_000249.4(MLH1):c.2040C>T (p.Cys680=)
NC_000003.12:g.37048954C>T
CM000665.2:g.37048954C>T
NC_000003.11:g.37090445C>T
CM000665.1:g.37090445C>T
NC_000003.10:g.37065449C>T
NG_007109.2:g.60605C>T
ENST00000413740.2:c.1668-1532C>T
ENST00000429117.6:c.1746C>T
ENST00000450420.6:c.1559-1532C>T
ENST00000456676.7:c.1896+1271C>T
ENST00000492474.6:c.1317C>T
ENST00000616768.6:c.1947C>T
ENST00000673673.2:c.1875C>T
ENST00000231790.8:c.2040C>T
ENST00000413212.2:c.*958C>T
ENST00000432299.6:c.*1872C>T
ENST00000447829.6:c.*1151C>T
ENST00000539477.6:c.1317C>T
ENST00000616768.5:c.984C>T
ENST00000673673.1:c.1828C>T
ENST00000673741.1:n.1074C>T
ENST00000673889.1:n.1422C>T
ENST00000673897.1:c.*1832C>T
ENST00000673899.1:c.1308C>T
ENST00000673947.1:c.*2180C>T
ENST00000673972.1:c.*1918C>T
ENST00000674019.1:c.1317C>T
ENST00000674111.1:c.*269C>T
ENST00000674125.1:n.751C>T
ENST00000231790.6:c.2040C>T
ENST00000413740.1:c.291-1532C>T
ENST00000435176.5:c.1746C>T
ENST00000450420.5:c.182-1532C>T
ENST00000455445.6:c.1317C>T
ENST00000456676.6:c.1871+1271C>T
ENST00000458205.6:c.1317C>T
ENST00000536378.5:c.1317C>T
ENST00000539477.5:c.1317C>T
NM_000249.3:c.2040C>T
NM_001167617.1:c.1746C>T
NM_001167618.1:c.1317C>T
NM_001167619.1:c.1317C>T
NM_001258271.1:c.1896+1271C>T
NM_001258273.1:c.1317C>T
NM_001258274.1:c.1317C>T
NM_001167617.2:c.1746C>T
NM_001167618.2:c.1317C>T
NM_001167619.2:c.1317C>T
NM_001258274.2:c.1317C>T
NM_001354615.1:c.1317C>T
NM_001354616.1:c.1317C>T
NM_001354617.1:c.1317C>T
NM_001354618.1:c.1317C>T
NM_001354619.1:c.1317C>T
NM_001354620.1:c.1746C>T
NM_001354621.1:c.1017C>T
NM_001354622.1:c.1017C>T
NM_001354623.1:c.1017C>T
NM_001354624.1:c.966C>T
NM_001354625.1:c.966C>T
NM_001354626.1:c.966C>T
NM_001354627.1:c.966C>T
NM_001354628.1:c.1947C>T
NM_001354629.1:c.1941C>T
NM_001354630.1:c.1875C>T
NM_001167617.3:c.1746C>T
NM_001167618.3:c.1317C>T
NM_001167619.3:c.1317C>T
NM_001258271.2:c.1896+1271C>T
NM_001258273.2:c.1317C>T
NM_001258274.3:c.1317C>T
NM_001354615.2:c.1317C>T
NM_001354616.2:c.1317C>T
NM_001354617.2:c.1317C>T
NM_001354618.2:c.1317C>T
NM_001354619.2:c.1317C>T
NM_001354620.2:c.1746C>T
NM_001354621.2:c.1017C>T
NM_001354622.2:c.1017C>T
NM_001354623.2:c.1017C>T
NM_001354624.2:c.966C>T
NM_001354625.2:c.966C>T
NM_001354626.2:c.966C>T
NM_001354627.2:c.966C>T
NM_001354628.2:c.1947C>T
NM_001354629.2:c.1941C>T
NM_001354630.2:c.1875C>T
More

Likely Benign

Met criteria codes 3
BP7 BP4 PM2_Supporting
Not Met criteria codes 1
BP5

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 MLH1 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 MLH1 c.2040C>T variant is predicted as a synonymous variant, p.(Cys680=). It is extremely rare in gnomAD v2.1.1 using the non-cancer dataset and in gnomAD v4.1 (<1 in 50,000 alleles: <0,002%). It is not predicted to affect splicing (predictions from http://priors.hci.utah.edu/PRIORS and SpliceAI). Therefore, this variant is classified as likely benign. (VCEP specifications version 1)
Met criteria codes
BP7
BP7 is assigned because it is a synonymous variant.
BP4
Splicing predictors do not predict any effect (max Splice-AI value= 0.02 and Prior_utah_splicing_de_novo=0.02 ).
PM2_Supporting
The variant is observed in 1.1e-05 frequency (Update: gnomAD v4.1 Grpmax AF = 0.00001583)
Not Met criteria codes
BP5
1 CRC cancer showing MSS/IHC normal (LOVD)
Curation History
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