rs267607735

chr3-37001058-G-Achr3-37001058-G-C

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.306+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000284 in 1,407,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: MLH1 NM_000249.4 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 0.9992
• Clinical Significance: Pathogenic reviewed by expert panel P:8 O:1
• Conservation: PhyloP100: 8.96

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, max_spliceai. No scorers claiming Uncertain. Scorers claiming Benign: dbscSNV1_RF.
• PP5: Variant 3-37001058-G-A is Pathogenic according to our data. Variant chr3-37001058-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 90148.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37001058-G-A is described in Lovd as [Pathogenic]. Variant chr3-37001058-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.306+5G>A		splice_donor_5th_base_variant, intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.306+5G>A		splice_donor_5th_base_variant, intron_variant		1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000284 AC: 4 AN: 1407220 Hom.: 0 Cov.: 25 AF XY: 0.00000426 AC XY: 3 AN XY: 703416

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000282

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 03, 2023	Common founder variant in the Spanish population (Borras et al., 2010); Intronic +5 splice variant in a gene for which loss-of-function is a known mechanism of disease, demonstrated to result in impaired splicing and aberrant transcript (Perez-Cabornero et al., 2009; Borras et al., 2010); Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Martinez-Bouzas et al., 2009; Perez-Carbonero et al., 2013); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 21778331, 22864660, 19250818, 25525159, 16142001, 28874130, 19760518, 24344984, 23554159, 25345868, 21972078, 23523604, 20858721) -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 02, 2021	This variant causes a G to A nucleotide substitution at the +5 position of intron 3 of the MLH1 gene. Functional RNA studies have shown that this variant causes use of a cryptic site in exon 3 resulting in premature truncation. This variant has been reported in multiple individuals affected with Lynch syndrome (PMID: 16142001, 19760518, 20858721, 23523604, 28874130) and is a common pathogenic variant in people of Spanish ancestry. 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 31, 2023	The c.306+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 3 in the MLH1 gene. This mutation has been identified in numerous families fulfilling Amsterdam I/II criteria and in individuals with tumors demonstrating high microsatellite instability (MSI-H) and/or loss of MLH1/PMS2 protein expression on immunohistochemistry (IHC) (Borras et al. Cancer Res 2010 Oct 1; 70(19):7379-91; Perez-Cabornero et al. Eur J Cancer 2009 May; 45(8): 1485-93, Pérez-Cabornero et al. J Mol Diagn 2013 May;15(3):380-90; Rossi BM et al. BMC Cancer, 2017 Sep;17:623, Ambry internal data). RNA analyses by these authors have demonstrated that this mutation generates an aberrant mRNA transcript resulting in premature protein truncation. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Haplotype analysis supports c.306+5G>A as a founder mutation of Spanish origin (Borras et al. Cancer Res 2010 Oct 1; 70(19):7379-91). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Oct 01, 2010

- -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant causes splicing aberration leading to truncated protein, >2 MSI-H tumours, co-segregation with disease & MAF 0.0 -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 16, 2023

This sequence change falls in intron 3 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. It affects a nucleotide within the consensus splice site. For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies have shown that this variant affects MLH1 function (PMID: 19250818). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 90148). This variant is also known as IVS3+5G>A. This variant has been observed in individuals with Lynch syndrome (PMID: 16142001, 23523604, 28874130). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). -

Lynch syndrome 1 Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
Cadd	Benign	19
Dann	Benign	0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Benign	0.62
SpliceAI score (max)		0.81		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.81		Position offset: -5

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

Publications

LitVar

Other links and lift over

dbSNP: rs267607735; hg19: chr3-37042549;