chr3-37017504-A-G

Variant names:

• chr3-37017504-A-G
• rs267607794
• NM_000249.4:c.791-2A>G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000249.4(MLH1):​c.791-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 8.59

Genes affected

MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.04139146 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.5, offset of 12, new splice context is: ttgtttggatcgtctggtAGaat. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37017504-A-G is Pathogenic according to our data. Variant chr3-37017504-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90372.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37017504-A-G is described in Lovd as [Pathogenic]. Variant chr3-37017504-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.791-2A>G		splice_acceptor_variant, intron_variant	Intron 9 of 18	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.791-2A>G		splice_acceptor_variant, intron_variant	Intron 9 of 18	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Jul 18, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 27363726]. -

Apr 12, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:2

Mar 20, 2019

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.791-2A>G variant in MLH1 has been reported in at least 4 individuals with Lynch syndrome-related cancers (Samowitz 2001, Parc 2003, Sjursen 2010, Susswein 2015) and in ClinVar (Variation ID: 90372). It was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Furthermore, this variant was found in probands with MSI-high and MLH1-absent colorectal cancers (Samowitz 2001, Sjursen 2010). Loss of function of the MLH1 gene is an established disease mechanism in autosomal dominant Lynch syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP criteria applied: PVS1, PM2, PS3_Supporting, PS4_Supporting. -

Jun 21, 2019

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Interrupts canonical donor splice site -

Hereditary cancer-predisposing syndrome Pathogenic:2

Mar 19, 2021

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes an A to G nucleotide substitution at the -2 position of intron 9 splice acceptor site of the MLH1 gene. This variant is predicted to impair RNA splicing with a likely consequence of out-of-frame skipping of exon 9. RNA studies have demonstrated that this variant results in abnormal splicing (ClinVar SCV000213526.5). This variant has been reported in individuals affected with Lynch syndrome (PMID: 11606497, 12624141, 20587412, 21642682, 30877237) or Lynch syndrome-associated cancers (PMID: 26681312, 29345684). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Aug 04, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.791-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides before coding exon 10 of the MLH1 gene. This alteration was reported in a 56 year old female diagnosed with colon cancer who had many first degree relatives affected with Lynch syndrome associated cancers; more than half of these family members were diagnosed before the age of 50 (Samowitz et al. Gastroenterology. 2001 Oct;121(4):830-8). This alteration was also reported in a Norwegian family that met Amsterdam criteria and had absent MLH1 and PMS2 staining on immunohistochemistry, as well as in a French family that met Amsterdam criteria (Parc Y et al. J Med Genet. 2003 Mar;40(3):208-13; Sjursen et al. J Med Genet. 2010 Sep;47(9):579-85). RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

not provided Pathogenic:1

Feb 07, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Reported in individuals with personal and/or family history of Lynch-related cancers with at least one tumor showing loss of MLH1 and PMS2 expression (Samowitz et al., 2001; Parc et al., 2003; Sjursen et al., 2010; Bonadona et al., 2011); This variant is associated with the following publications: (PMID: 15331927, 21642682, 25525159, 26681312, 20587412, 12624141, 28152038, 11606497, 30787465) -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Jul 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects an acceptor splice site in intron 9 of the MLH1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Lynch syndrome (PMID: 11606497, 12624141, 20587412, 21642682; Invitae). It has also been observed to segregate with disease in related individuals. Invitae’s Lynch syndrome clinical variant model, which takes into account the clinical and family history, age, sex, and reported ancestry of multiple individuals with this MLH1 variant, predicts that it is pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model developed at Invitae that incorporates the clinical features of 1,370,736 individuals referred for testing at Invitae. This variant is also known as IVS9-2A>G. ClinVar contains an entry for this variant (Variation ID: 90372). Studies have shown that disruption of this splice site results in skipping of exon 10, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 22949379; Invitae). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	30
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.99
FATHMM_MKL	Pathogenic	1.0	D
GERP RS		5.4

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.19		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267607794; hg19: chr3-37058995; COSMIC: COSV51622746; COSMIC: COSV51622746;