rs41294980

chr3-37025815-G-Achr3-37025815-G-Cchr3-37025815-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1 BP4_Strong BP6_Very_Strong BS1

The NM_000249.4(MLH1):c.1217G>A(p.Ser406Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,613,824 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S406G) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00084 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0011 (2 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Benign reviewed by expert panel U:3 B:25 O:1
• Conservation: PhyloP100: 2.95

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 Benign. Variant got -14 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 15 uncertain in NM_000249.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.01582715).
• BP6: Variant 3-37025815-G-A is Benign according to our data. Variant chr3-37025815-G-A is described in ClinVar as [Benign]. Clinvar id is 41634.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37025815-G-A is described in Lovd as [Benign]. Variant chr3-37025815-G-A is described in Lovd as [Pathogenic]. Variant chr3-37025815-G-A is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000842 (128/151934) while in subpopulation NFE AF= 0.00143 (97/67960). AF 95% confidence interval is 0.0012. There are 0 homozygotes in gnomad4. There are 60 alleles in male gnomad4 subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1217G>A	p.Ser406Asn	missense_variant	12/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1217G>A	p.Ser406Asn	missense_variant	12/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes AF: 0.000843 AC: 128 AN: 151816 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000789

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00143

Gnomad OTH AF: 0.00336

GnomAD3 exomes AF: 0.000883 AC: 222 AN: 251336 Hom.: 0 AF XY: 0.000942 AC XY: 128 AN XY: 135834

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.00133

Gnomad ASJ exome AF: 0.000794

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000327

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.00123

Gnomad OTH exome AF: 0.00212

GnomAD4 exome AF: 0.00106 AC: 1543 AN: 1461890 Hom.: 2 Cov.: 34 AF XY: 0.00108 AC XY: 784 AN XY: 727248

Gnomad4 AFR exome AF: 0.000119

Gnomad4 AMR exome AF: 0.00125

Gnomad4 ASJ exome AF: 0.000497

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000301

Gnomad4 FIN exome AF: 0.0000749

Gnomad4 NFE exome AF: 0.00123

Gnomad4 OTH exome AF: 0.00109

GnomAD4 genome AF: 0.000842 AC: 128 AN: 151934 Hom.: 0 Cov.: 31 AF XY: 0.000808 AC XY: 60 AN XY: 74272

Gnomad4 AFR AF: 0.000217

Gnomad4 AMR AF: 0.000788

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00143

Gnomad4 OTH AF: 0.00332

Alfa AF: 0.00125 Hom.: 0

Bravo AF: 0.000786

TwinsUK AF: 0.00189 AC: 7

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00198 AC: 17

ExAC AF: 0.000931 AC: 113

EpiCase AF: 0.00120

EpiControl AF: 0.00119

ClinVar

Significance: Benign

Submissions summary: Uncertain:3 Benign:25 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not specified Uncertain:1 Benign:9 Other:1

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 20, 2014	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 10, 2017	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: This variant is present at 0.13% in gnomAD (171/126520 European chrs). It is classified in ClinVar with 3 stars as Likely benign or benign by InSiGHT (Expert panel), Invitae, GeneDx, Ambry, Emory, Mayo, and as VUS by Biesecker lab. It is not a poorly conserved AA but no species has Asn at this position. It is present in 15 papers in HGMD (classified as DM?), most comments say it is not pathogenic. -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 30, 2021	- -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 19, 2013	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -

not provided Uncertain:1 Benign:4

Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Apr 06, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 07, 2016	Variant summary: The MLH1 c.1217G>A variant affects a non-conserved nucleotide, resulting in an amino acid change from Ser to Asn. 4/4 in-silico tools predict benign outcome for this variant (SNPs&GO not captured due to low reliability index). In vitro MMR assay has shown that this variant has ~75% of wild-type activity and interacts with EXO1 and PMS2 similar to wild-type in a yeast two-hybrid assay. This variant is found in 115/123542 control chromosomes at a frequency of 0.0009309, which exceeds the maximal expected frequency of a pathogenic allele (0.0007105). Additionally, multiple reputable diagnostic labs and databases have classified this variant as benign/neutral. Taken together, this variant was classified as benign. -
Uncertain significance, no assertion criteria provided	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jul 13, 2012	- -
Benign, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	MLH1: BP4, BS3:Moderate, BS1 -

Hereditary cancer-predisposing syndrome Benign:4

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 07, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 18, 2014	This alteration is classified as 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. -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	Nov 19, 2020	- -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Jul 13, 2018	- -

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

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 12, 2018	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. -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

Lynch syndrome Benign:2

Benign, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Multifactorial likelihood analysis posterior probability <0.001 -
Likely benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	- -

Breast and/or ovarian cancer Benign:1

Likely benign, criteria provided, single submitter

clinical testing

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

Oct 19, 2022

- -

Carcinoma of colon Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

 The MLH1 p.Ser406Asn variant was identified in 6 of 4978 proband chromosomes (frequency: 0.001) from Danish, Spanish, Scottish, Korean, Italian and American individuals or families with  HNPCC, or sporadic CRC (Nilbert 2009, Martinez-Bouzas 2009, Kim 2004, Cunningham 2001, Perez-Cabornero 2013, Genuardi  1999, Barnetson 2008). Multiple functional assays  show the variant to be MMR proficient (Drost 2009, Kondo  2003, Takahashi  2007, Wanat 2007). Bioinformatic algorithms suggest the variant is a uncertain significance, with the MAPP-MMR (multivariate analysis of protein polymorphism) score of 1.07, and class 2 by IARC (Chao 2008, Pastrello 2011).   The variant was also identified in the following databases: dbSNP (ID: rs41294980) “With other allele”, ClinVar (classifed benign, reviewed by an expert panel (2013); submitters: benign by InSIGHT, Invitae, GeneDx, Ambry Genetics, Mayo Clinic; uncertain significance by Laboratory for Molecular Medicine (Partners HealthCare Personalized Medicine) and Biesecker Lab/Human Development Section (NIH); likely benign by EGL Genetic Diagnostics (Eurofins Clinical Diagnostics) and classification not provided by ITMI), UMD-LSDB (1x as neutral), Insight Colon Cancer Gene Variant Database (43x class 1), Mismatch Repair Genes Variant Database, Insight Hereditary Tumors Database (44x). The variant was not identified in the COGR, Cosmic, MutDB, and Zhejiang Colon Cancer Databases. The variant was identified in control databases in 249 of 276804 chromosomes at a frequency of 0.0009 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), and was identified in the following populations: African in 5 of 23990 chromosomes (frequency: 0002), Other in 14 of 6448 chromosomes (frequency: 002), Latino in 38 of 34410 chromosomes (frequency: 001), European Non-Finnish in 172 of 126420 chromosomes (frequency: 001), Ashkenazi Jewish in 8 of 10140 chromosomes (frequency: 00085), European Finnish in 2 of 25748 chromosomes (frequency: 00008), South Asian in 10 of 30782 chromosomes (frequency: 0003). The p.Ser406 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. -

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

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jan 10, 2022

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.15
Cadd	Benign	14
Dann	Benign	0.95
DEOGEN2	Benign	0.27	T;.;.;.;.;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.41
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.51	T;T;.;.;.;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.016	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	L;.;.;.;.;.
MutationTaster	Benign	1.0	N;N;N;N;N;N
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.46	N;N;N;N;N;N
REVEL	Uncertain	0.39
Sift	Benign	0.26	T;T;T;T;T;T
Sift4G	Benign	0.53	T;T;T;T;T;T
Polyphen		0.38	B;.;.;.;.;.
Vest4		0.31
MVP		0.85
MPC		0.072
ClinPred		0.0049	T
GERP RS		2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.026
gMVP		0.19

Splicing

Name	Calibrated prediction	Score	Prediction
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

Publications

LitVar

Other links and lift over

dbSNP: rs41294980; hg19: chr3-37067306; COSMIC: COSV51621063; COSMIC: COSV51621063;