3-37017603-A-G

Position:

• chr3-37017603-A-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000249.4(MLH1):​c.884+4A>G variant causes a splice donor region, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9903
• Clinical Significance: Pathogenic reviewed by expert panel P:6
• Conservation: PhyloP100: 4.51

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 3-37017603-A-G is Pathogenic according to our data. Variant chr3-37017603-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 90414.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37017603-A-G is described in Lovd as [Pathogenic]. Variant chr3-37017603-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.884+4A>G		splice_donor_region_variant, intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.884+4A>G		splice_donor_region_variant, intron_variant		1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 18, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 18561205, 17653898]. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jun 16, 2021	- -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant allele results in splicing abberation leading to premature stop codon: full inactivation of variant allele -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Apr 03, 2023

Non-canonical splice site variant demonstrated to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease (Rahner et al., 2007; Tournier et al., 2010); Not observed in large population cohorts (gnomAD); Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Rahner et al., 2007; Barrow et al., 2010; Kim et al., 2010; Pastrello et al., 2011; Yurgelun et al., 2015; Patel et al., 2021); This variant is associated with the following publications: (PMID: 21239990, 25525159, 18561205, 21034533, 20459533, 17653898, 19339519, 24333619, 33436027, 25980754) -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 11, 2023

This sequence change falls in intron 10 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with MLH1-related conditions (PMID: 17653898, 18561205, 21239990, 25980754). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS10+4A>G. ClinVar contains an entry for this variant (Variation ID: 90414). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in exon 10 skipping and introduces a premature termination codon (PMID: 1856120, 17653898). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant disrupts the p.Arg265 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24344984, 28874130). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 10, 2024

The c.884+4A>G intronic pathogenic mutation results from an A to G substitution four nucleotides after coding exon 10 in the MLH1 gene. In one study, this variant was observed in two individuals fulfilling Bethesda criteria, whose tumors showed high microsatellite instability (MSI-H) and absence of MLH1 staining on immunohistochemistry. Furthermore, the variant was observed to segregate with colon cancer in the father and sister of one proband (Rahner N et al. Acta Oncol. 2007;46(6):763-9). This variant was also identified in an Italian proband whose tumor was MSI-H (Pastrello C et al. Genet Med, 2011 Feb;13:115-24). In silico splice site analysis for this alteration is inconclusive. Functional splicing analysis by RT-PCR using patient samples and in a mini gene assay demonstrated exon 10 skipping was associated with this variant (Rahner N et al. Acta Oncol. 2007;46(6):763-9; Tournier I et al. Hum. Mutat. 2008;29(12):1412-24; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	23
DANN	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.80
SpliceAI score (max)		0.29		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.29		Position offset: -4

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

Publications

LitVar

Other links and lift over

dbSNP: rs267607777; hg19: chr3-37059094;