rs369521379

Variant names:

• chr3-37007063-G-A
• rs369521379
• ENST00000458205.6:c.-271G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-37007063-G-A
• chr3-37007063-G-C
• chr3-37007063-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PP3_Moderate

The ENST00000458205.6(MLH1):​c.-271G>A variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,610,186 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 Uncertain significance (★★★).

• Frequency:
  • Genomes: 𝑓 0.000059 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000025 (0 hom.)
• Consequence: MLH1 ENST00000458205.6 splice_region
• Scores: Splicing: ADA: 0.9998
• Clinical Significance: Uncertain significance reviewed by expert panel U:16 B:2
• Conservation: PhyloP100: 0.311
• Publications: 7 publications found

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]

MLH1 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet
• Lynch syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
• Muir-Torre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• Lynch syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• ovarian cancer

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• rhabdomyosarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• breast cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458205.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	NM_000249.4	MANE Select	c.453G>A	p.Thr151Thr	splice_region synonymous	Exon 5 of 19	NP_000240.1
	MLH1	NM_001167618.3		c.-271G>A		splice_region	Exon 5 of 19	NP_001161090.1
	MLH1	NM_001167619.3		c.-179G>A		splice_region	Exon 5 of 18	NP_001161091.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000458205.6	TSL:1	c.-271G>A		splice_region	Exon 6 of 20	ENSP00000402667.2
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.453G>A	p.Thr151Thr	splice_region synonymous	Exon 5 of 19	ENSP00000231790.3
	MLH1	ENST00000456676.7	TSL:1	c.453G>A	p.Thr151Thr	splice_region synonymous	Exon 5 of 17	ENSP00000416687.3

Frequencies

GnomAD3 genomes AF: 0.0000592 AC: 9 AN: 152116 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00000796 AC: 2 AN: 251372 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000247 AC: 36 AN: 1458070 Hom.: 0 Cov.: 28 AF XY: 0.0000220 AC XY: 16 AN XY: 725652

African (AFR) AF: 0.0000599 AC: 2 AN: 33410

American (AMR) AF: 0.0000447 AC: 2 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26116

East Asian (EAS) AF: 0.000328 AC: 13 AN: 39668

South Asian (SAS) AF: 0.00 AC: 0 AN: 86164

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53384

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5760

European-Non Finnish (NFE) AF: 0.0000153 AC: 17 AN: 1108574

Other (OTH) AF: 0.0000332 AC: 2 AN: 60280

GnomAD4 genome AF: 0.0000592 AC: 9 AN: 152116 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74296

African (AFR) AF: 0.000145 AC: 6 AN: 41424

American (AMR) AF: 0.00 AC: 0 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5194

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68014

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.0000533 Hom.: 0

Bravo AF: 0.0000907

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:16 Benign:2

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:3 Benign:1

Jan 17, 2024

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nov 19, 2024

Myriad Genetics, Inc.

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].

Aug 19, 2021

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MLH1 c.453G>A (p.Thr151=) synonymous change has a maximum subpopulation frequency of 0.0040% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/3-37048554-G-A). Algorithms that predict the impact of sequence changes on splicing indicate that this change may create or strengthen a splice site (PP3), but this prediction has not been confirmed by RNA studies. This variant has been reported in individuals with colorectal cancer and/or clinical features of Lynch syndrome (PMID: 26845104, 28449805, 33309985), individuals with other cancers (PMID: 31386297, 32634176), and in a tumor that demonstrated loss-of-heterozygosity of the wild-type allele (PMID: 29887214). It has also been reported in non-cancer controls (PMID: 33309985). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PP3.

Apr 20, 2020

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not specified Uncertain:3

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Feb 21, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Thr151Thr variant in MLH1 has been reported in one individual with colorec tal polyps and a family history of colorectal cancer (Shirts 2016). This variant has been identified in 1/16492 of South Asian chromosomes by the Exome Aggregat ion Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs369521379). Althou gh the p.Thr151Thr variant does not alter an amino acid residue, it is located i n the last base of the exon, which is part of the 5? splice region. Computationa l tools suggest some impact to splicing though this information is not predictiv e enough to determine pathogenicity. In contrast, this variant has been classifi ed as Likely Pathogenic on Sept 5, 2013 by the ClinGen-approved InSiGHT expert p anel (ClinVarSCV000106723.2), due a predicted splicing effect that has not been confirmed by published functional studies. In summary, the clinical significance of the p.Thr151Thr variant is uncertain.

Feb 06, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.453G>A (p.Thr151Thr) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes the canonical 5' splicing donor site. One predict the variant creates a 3' acceptor site. Three predict the variant weakens the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8e-06 in 251372 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.453G>A has been reported in the literature in individuals affected with/undergoing testing for Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome or other cancers and also as a VUS in settings of multigene panel testing in individuals with colorectal cancer and Breast and/or ovarian cancer (example, Shirts_2016, Sunga_2017, Kiyozumi_2019, Molina-Zayas_2022). A large case-control study evaluating Biliary tract cancer reported the variant insignificantly distributed between cases and controls (Okawa_2023). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome. At-least one co-occurrence with another pathogenic variant has been observed at our laboratory (BRCA1 c.188T>A, p.Leu63Ter), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31386297, 35451682, 36243179, 26845104, 28449805). ClinVar contains an entry for this variant (Variation ID: 90229). Based on the evidence outlined above, the variant was classified as uncertain significance.

not provided Uncertain:3

Apr 04, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MLH1 c.453G>A (p.Thr151=) synonymous variant has been reported in the published literature in individuals with Lynch Syndrome and/or a personal history of polyps (PMIDs: 28449805 (2017), 26845104 (2016)), pancreatic cancer (PMID: 32980694 (2020)), breast and ovarian cancer (PMID: 32634176 (2020)), and in at least one reportedly healthy individual (PMID: 32980694 (2020)). The frequency of this variant in the general population, 0.000011 (3/282760 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper MLH1 mRNA splicing. Based on the available information, we are unable to determine the clinical significance of this variant.

Aug 10, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Observed in individuals with Lynch-related and other cancers as well as polyps, but also in cancer-free controls (Shirts et al., 2016; Sunga et al., 2017; Matejcic et al., 2020; Singh et al., 2020; Okawa et al., 2023); This variant is associated with the following publications: (PMID: 32832836, 28449805, 31386297, 12414824, 26845104, 30720243, 35451682, 36243179, 32634176, 33309985)

Oct 24, 2016

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Hereditary cancer-predisposing syndrome Uncertain:3

Sep 11, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.453G>A variant (also known as p.T151T) located in coding exon 5 of the MLH1 gene. This variant results from a G to A substitution at nucleotide position 453. This nucleotide substitution does not change the threonine at codon 151. However, this change occurs in the last base pair of exon 5 which makes it likely to have some effect on normal mRNA splicing. This alteration has been detected in numerous individuals who do not have a personal or family history that is consistent with or suggestive of hereditary nonpolyposis colorectal cancer (HNPCC)/Lynch syndrome (Ambry internal data). This alteration has been identified in an individual suspected of having Lynch syndrome, an individual with polyps, and a woman with endometrial cancer (Sunga AY et al. Cancer Genet, 2017 04;212-213:1-7; Shirts BH et al. Genet. Med., 2016 10;18:974-81; Singh AK et al. PLoS One, 2020 Jul;15:e0235613). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may result in the creation or strengthening of a novel splice donor site. RNA studies have demonstrated an incomplete splice defect for this alteration resulting in a transcript predicted to lead to a protein with an in-frame insertion of 3 amino acids; however, the exact functional impact of the inserted amino acids is unknown at this time (Ambry internal data). Based on the available evidence, the clinical significance of this variant remains unclear.

Apr 25, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This synonymous variant does not change the amino acid sequence of the MLH1 protein, but does change the last nucleotide of exon 5. Splice site prediction tools suggest that this variant may impact RNA splicing. However, this prediction has not been confirmed in published RNA studies. This variant has been reported in individuals affected with polyps (PMID: 26845104), lung cancer (PMID: 31386297), breast/ovarian cancer (PMID: 32068069), endometrial cancer (PMID: 32634176), and in a cohort of individuals affected with suspected Lynch syndrome (PMID: 28449805). However, case-control studies have reported no association with colorectal (PMID: 33309985), biliary tract (PMID: 36243179), or pancreatic cancer (PMID: 32980694). This variant has also been identified in 3/282760 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

Sep 18, 2021

Sema4, Sema4

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

Breast and/or ovarian cancer Uncertain:1

Mar 03, 2021

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1

Dec 08, 2022

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

Lynch syndrome 1 Uncertain:1

Jun 13, 2018

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: curation

Criteria changed for variants in last base of exon therefore downgrade classification

Lynch syndrome Uncertain:1

May 01, 2018

University of Washington Department of Laboratory Medicine, University of Washington

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MLH1 NM_000249.3:c.453G>A has a 75.7% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 0.16 to 1, generated from evidence of seeing this as a somatic mutation in a tumor with loss of heterozygosity at the MLH1 locus. See Shirts et al 2018, PMID 29887214. This was also reported in Shirts et al 2016, PMID 26845104 in an individual with a family history of colorectal cancer.

Hereditary nonpolyposis colorectal neoplasms Benign:1

Dec 12, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Uncertain	23
DANN	Benign	0.85
PhyloP100		0.31
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.9
Mutation Taster		=32/68	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.31		Position offset: 9

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

Other links and lift over

dbSNP: rs369521379; hg19: chr3-37048554;