3-37025958-G-C

Variant names:

• chr3-37025958-G-C
• rs63750527
• NM_000249.4:c.1360G>C

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Moderate BP6 BS1

The NM_000249.4(MLH1):​c.1360G>C​(p.Gly454Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000905 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Synonymous variant affecting the same amino acid position (i.e. G454G) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000079 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000092 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:9 B:13
• Conservation: PhyloP100: 0.405
• Publications: 19 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: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10145408).
• BP6: Variant 3-37025958-G-C is Benign according to our data. Variant chr3-37025958-G-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 89705.
• BS1: Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.0000917 (134/1461882) while in subpopulation MID AF = 0.00208 (12/5768). AF 95% confidence interval is 0.0012. There are 0 homozygotes in GnomAdExome4. There are 75 alleles in the male GnomAdExome4 subpopulation. Median coverage is 34. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000249.4. 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.1360G>C	p.Gly454Arg	missense	Exon 12 of 19	NP_000240.1
	MLH1	NM_001354628.2		c.1360G>C	p.Gly454Arg	missense	Exon 12 of 18	NP_001341557.1
	MLH1	NM_001354629.2		c.1261G>C	p.Gly421Arg	missense	Exon 11 of 18	NP_001341558.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.1360G>C	p.Gly454Arg	missense	Exon 12 of 19	ENSP00000231790.3
	MLH1	ENST00000456676.7	TSL:1	c.1360G>C	p.Gly454Arg	missense	Exon 12 of 17	ENSP00000416687.3
	MLH1	ENST00000413740.2	TSL:1	c.1360G>C	p.Gly454Arg	missense	Exon 12 of 15	ENSP00000416476.2

Frequencies

GnomAD3 genomes AF: 0.0000789 AC: 12 AN: 152106 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.000957

GnomAD2 exomes AF: 0.000120 AC: 30 AN: 250988 AF XY: 0.000125

Gnomad AFR exome AF: 0.0000624

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: 0.000159

Gnomad OTH exome AF: 0.000164

GnomAD4 exome AF: 0.0000917 AC: 134 AN: 1461882 Hom.: 0 Cov.: 34 AF XY: 0.000103 AC XY: 75 AN XY: 727246

African (AFR) AF: 0.000209 AC: 7 AN: 33480

American (AMR) AF: 0.0000671 AC: 3 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000232 AC: 20 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00208 AC: 12 AN: 5768

European-Non Finnish (NFE) AF: 0.0000728 AC: 81 AN: 1112004

Other (OTH) AF: 0.000182 AC: 11 AN: 60394

GnomAD4 genome AF: 0.0000788 AC: 12 AN: 152224 Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4 AN XY: 74438

African (AFR) AF: 0.0000482 AC: 2 AN: 41530

American (AMR) AF: 0.0000654 AC: 1 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10592

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68028

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.000203 Hom.: 0

Bravo AF: 0.0000945

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ExAC AF: 0.000148 AC: 18

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000273

EpiControl AF: 0.000415

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:9 Benign:13

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:2 Benign:4

Aug 01, 2018

GeneKor MSA

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Feb 12, 2021

Sema4, Sema4

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: curation

Aug 23, 2018

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

May 05, 2025

Molecular Diagnostics Laboratory, Catalan Institute of Oncology

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BS1, BP4 c.1360G>C, located in exon 12 of the MLH1 gene, is predicted to result in the substitution of glycine by arginine at codon 454, p.(Gly454Arg). The variant allele was found in 146/1614106 alleles, with a filter allele frequency of 0,015% within the South Asian population in the gnomAD v4.1.0 database (BS1). Computational tools for this variant suggest no significant impact on splicing and does not affect the protein function (MAPP+PolyPhen-2 prior probability for pathogenicity: 0.00) (BP4). A minigene assay of this variant did not detect aberrant splicing (PMID: 16395668). This variant has been reported in patients with MSS CRC and no MLH1 loss (PMID: 20020535, internal data), as well as in a patient with EC showing loss of MLH1 and PMS2 protein expression by IHC (internal data). This variant has been reported in the ClinVar database (3x benign, 8x likely benign, 8x uncertain significance), it has not been reported in LOVD, and it has been classified as uncertain significance by InSiGHT. Based on currently available information, the variant c.1360G>C should be considered a likely benign variant according to ClinGen CRC ACMG Specifications MLH1 v1.0.0.

Sep 26, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jul 13, 2025

Laboratorio de I+D, Fundación Centro Médico de Asturias

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BP4_Moderate+PM1_Supporting+PM2_Supporting

not provided Uncertain:2 Benign:2

Sep 24, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 30998989, 28874130, 25929848, 27150160, 12624141, 18383312, 22290698, 16395668, 25133505, 21404117, 31159747)

Nov 12, 2019

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Sep 22, 2017

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MLH1 c.1360G>C;p.Gly454Arg is reported in the medical literature in individuals with Lynch syndrome (Auclair 2006, Lucci-Cordisco 2006, Loizidou 2014, and Hardt 2011). multiple computational analyses indicate the variant has a neutral effect on the MLH1 protein (Chao 2008). This variant is listed in the dbSNP variant database (rs63750527) and in the Genome Aggregation Database in 28 individuals (28 out of 277032 alleles). The p.Gly454Arg variant is classified by the International Society for Gastrointestinal Hereditary Tumours Incorporated (InSiGHT) as a variant of uncertain significance because there is insufficient evidence about this variant (Variation ID: 89705). The glycine at this position is weakly conserved across species and computational algorithms (AlignGVGD, Polyphen2, SIFT) predict this variant is tolerated. Considering available information, there is insufficient evidence to classify this variant with certainty. References: Chao et al. Accurate classification of MLH1/MSH2 missense variants with multivariate analysis of protein polymorphisms-mismatch repair (MAPP-MMR). Hum Mutat. 2008; 29(6):852-860. Hardt et al. Missense variants in hMLH1 identified in patients from the German HNPCC consortium and functional studies. Fam Cancer. 2011;10(2):273-284. Loizidou et al. The mutational spectrum of Lynch syndrome in cyprus. PLoS One. 2014; 9(8):e105501. Lucci-Cordisco et al. The use of microsatellite instability, immunohistochemistry and other variables in determining the clinical significance of MLH1 and MSH2 unclassified variants in Lynch syndrome. Cancer Biomark. 2006;2(1-2):11-27.

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Nov 23, 2015

Counsyl

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.

Apr 28, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Nov 27, 2024

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered 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]. This variant has been observed in conjunction with multiple pathogenic variants, reducing the likelihood this variant itself is pathogenic.

not specified Uncertain:1 Benign:2

Mar 31, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 1 paper in HGMD; ExAC: 6/16506 South Asian; ClinVar: 4 VUS (1 expert panel)

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

May 14, 2022

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.1360G>C (p.Gly454Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 250988 control chromosomes (gnomAD). This frequency is not higher than the expected maximum for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (0.00012 vs 0.00071), allowing no conclusion about variant significance. The variant, c.1360G>C, has been reported in the literature in individuals affected with tumors that belong to the Lynch syndrome tumor spectrum (e.g. Parc_2003, Auclair_2006, Hardt_2011, Loizidou_2014). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrences with other pathogenic variants have been reported (MSH2 c.1165C>T (p.Arg389X) in UMD; and BRCA1 c.3700_3704delGTAAA (p.Val1234fsX8), CHEK2 c.1169A>C (p.Tyr390Ser), MSH2 c.2006-2A>T at our laboratory), providing supporting evidence for a benign role. At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated no damaging effect of this variant (Bouvet_2019). Multiple submitters have provided clinical-significance assessments for this variant in ClinVar after 2014 without evidence for independent evaluation, and classified the variant as VUS (n=10) or likely benign/Benign (n=5). Based on the evidence outlined above, the variant was classified as benign.

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

Jan 03, 2024

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Oct 31, 2018

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MLH1-related disorder Uncertain:1

May 23, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The MLH1 c.1360G>C variant is predicted to result in the amino acid substitution p.Gly454Arg. This variant has been reported in individuals with non-polyposis colorectal cancer (Auclair et al. 2006. PubMed ID: 16395668; Loizidou et al. 2014. PubMed ID: 25133505; Rossi et al. 2017. PubMed ID: 28874130) or breast and/or ovarian cancer (Supplementary Table S5, Tsaousis et al. 2019. PubMed ID: 31159747; Supplementary Table 3, Guindalini et al. 2022. PubMed ID: 35264596). However, experimental studies suggest this variant does not impact protein function (Bouvet et al. 2019. PubMed ID: 30998989; Rath et al. 2022. PubMed ID: 36054288). This variant is reported in 0.029% of alleles in individuals of South Asian descent in gnomAD. In ClinVar, this variant is interpreted as benign/likely benign/uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89705/). This variant could be benign. However, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Breast and/or ovarian cancer Benign:1

Aug 31, 2021

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Hereditary nonpolyposis colon cancer Benign:1

Mar 06, 2022

Mendelics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Hereditary nonpolyposis colorectal neoplasms Benign:1

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	14
DANN	Benign	0.16
DEOGEN2	Benign	0.29	T
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.52	D
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.0	L
PhyloP100		0.41
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.41	N
REVEL	Uncertain	0.56
Sift	Benign	0.51	T
Sift4G	Benign	0.40	T
Polyphen		0.0	B
Vest4		0.23
MutPred		0.20		Gain of MoRF binding (P = 0.0202)
MVP		0.96
MPC		0.078
ClinPred		0.015	T
GERP RS		1.5
PromoterAI		0.050	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.017
gMVP		0.23
Mutation Taster		=79/21	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		1.0
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs63750527; hg19: chr3-37067449; COSMIC: COSV107225381;