rs267607735

Variant names:

• chr3-37001058-G-A
• rs267607735
• NM_000249.4:c.306+5G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-37001058-G-A
• chr3-37001058-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 region, 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_region, intron
• Scores: Splicing: ADA: 0.9992
• Clinical Significance: Pathogenic reviewed by expert panel P:9 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 rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.306+5G>A		splice_region_variant, intron_variant	Intron 3 of 18	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.306+5G>A		splice_region_variant, intron_variant	Intron 3 of 18	1	NM_000249.4	ENSP00000231790.3

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:9 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:3

Oct 27, 2024

Molecular Diagnostics Laboratory, Catalan Institute of Oncology

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting, PP1_Strong, PP3, PP4_Strong c.306+5G>A is an intronic variant located close to a canonical splice site. It is not present in the population database gnomAD v2.1.1, non-cancer dataset (PM2_supporting). The SpliceAI algorithm predicts the activation of a novel splicing donor site (deltascore: 0.81) (PP3_supporting). mRNA assays have reported a splicing effect (r.302_306del; p.Glu102Phefs*18) (PMID: 19250818, 20858721). This variant is considered a Spanish founder mutation, and it cosegregates with the disease in at least 5 informative meioses in more than 2 families (data from our internal cohort of patients) (PP1_Strong). Also, it has been reported in more than 3 independent CRC/Endometrial tumors showing MLH1/PMS2 loss in the absence of MLH1 methylation in more than 2 families (PMID: 20858721, 16142001, 19250818, 23523604 and internal data) (PP4_Strong). This variant has been reported in the ClinVar database (7x pathogenic), although not in LOVD, it has been classified by InSiGHT as pathogenic. Based on currently available information, the variant c.306+5G>A should be considered a pathogenic variant, according to ACMG/AMP guidelines. -

Jun 02, 2021

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Mar 31, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not provided Pathogenic:2

Jan 09, 2025

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Common founder variant in the Spanish population (PMID: 20858721); Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (PMID: 19760518, 23523604); 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 (PMID: 19250818; 20858721); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21778331, 22864660, 19250818, 25525159, 16142001, 28874130, 19760518, 24344984, 23554159, 25345868, 21972078, 16083711, 21120944, 22753075, 20858721, 23523604) -

-

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Oct 01, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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

Oct 31, 2018

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:1

Sep 05, 2013

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: research

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

Mar 06, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. This variant is not present in population databases (gnomAD no frequency). 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 also known as IVS3+5G>A. ClinVar contains an entry for this variant (Variation ID: 90148). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects MLH1 function (PMID: 19250818). 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. For these reasons, this variant has been classified as Pathogenic. -

Lynch syndrome 1 Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

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;