rs63750114

chr3-37049015-C-Achr3-37049015-C-Gchr3-37049015-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PM1 PM5 BP4_Strong BP6_Very_Strong BS1

The NM_000249.4(MLH1):c.2101C>A(p.Gln701Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000951 in 1,609,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q701H) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00021 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000083 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense, splice_region
• Scores: Splicing: ADA: 0.02623
• Clinical Significance: Likely benign reviewed by expert panel U:4 B:14
• Conservation: PhyloP100: 4.68

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 -12 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 15 uncertain in NM_000249.4
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37049017-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 90049.Status of the report is reviewed_by_expert_panel, 3 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.0071430206).
• BP6: Variant 3-37049015-C-A is Benign according to our data. Variant chr3-37049015-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 90042.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37049015-C-A is described in Lovd as [Likely_benign]. Variant chr3-37049015-C-A is described in Lovd as [Likely_pathogenic]. Variant chr3-37049015-C-A is described in Lovd as [Pathogenic].
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00021 (32/152288) while in subpopulation EAS AF= 0.00579 (30/5184). AF 95% confidence interval is 0.00416. There are 0 homozygotes in gnomad4. There are 21 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.2101C>A	p.Gln701Lys	missense_variant, splice_region_variant	18/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.2101C>A	p.Gln701Lys	missense_variant, splice_region_variant	18/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes AF: 0.000210 AC: 32 AN: 152170 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000491 AC: 123 AN: 250694 Hom.: 0 AF XY: 0.000443 AC XY: 60 AN XY: 135480

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00665

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000164

GnomAD4 exome AF: 0.0000830 AC: 121 AN: 1457284 Hom.: 0 Cov.: 30 AF XY: 0.0000744 AC XY: 54 AN XY: 725328

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00280

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.000133

GnomAD4 genome AF: 0.000210 AC: 32 AN: 152288 Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21 AN XY: 74476

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000466 Hom.: 0

Bravo AF: 0.000268

ExAC AF: 0.000453 AC: 55

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Uncertain:4 Benign:14

Revision: reviewed by expert panel

Submissions by phenotype

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

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	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	Mendelics	May 28, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Uncertain significance, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -

not provided Benign:3

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	May 18, 2020	This variant is associated with the following publications: (PMID: 16929514, 30521064, 23760103, 17011982, 18931482, 18726168, 18383312, 24933000, 22136435, 22995991, 18094436, 26811195, 23431106, 26900293, 26078562, 24710284, 23047549, 26332594, 29192238, 29050249, 25338684, 25479140, 29360550, 30093976, 31784484) -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MLH1 p.Gln701Lys variant was identified in 17 of 1894 proband chromosomes (frequency: 0.009) from individuals or families with Lynch syndrome or gastric cancer and was present in 3 of 1818 control chromosomes (frequency: 0.002) from healthy individuals (Chen 2013, Fan 2007, Sheng 2008, Talseth-Palmer 2016, Yap 2009, Zhang 2006, Zhi 2011). The variant was also identified in the following databases: dbSNP (ID: rs63750114) as "With Pathogenic, other allele", ClinVar (3x likely benign including InSiGHT expert panel, 2x benign, 2x uncertain significance), Clinvitae (4x), Cosmic (1x, confirmed somatic, in adenocarcinoma of large intestine), Insight Colon Cancer Gene Variant Database (10x, Likely not pathogenic/little clinical significance), Zhejiang Colon Cancer Database (4x), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (11x). The variant was not identified in MutDB or the UMD-LSDB database. The variant was identified in control databases in 129 of 276412 chromosomes at a frequency of 0.0005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 1 of 23994 chromosomes (freq: 0.00004), Other in 2 of 6450 chromosomes (freq: 0.0003), and East Asian in 126 of 18826 chromosomes (freq: 0.007). The variant was not observed in the Latino, European, Ashkenazi Jewish, Finnish, or South Asian populations. A functional study utilizing a yeast two-hybrid assay showed that MLH1 p.Gln701Lys interacts with PMS2 at reduced efficiency (16.6% relative activity in comparison with wild-type MLH1) (Fan 2007). In the same study, a co-immunoprecipitation assay demonstrated p.Gln701Lys retains 70% interaction with PMS2 (Fan 2007). Thus, the functional studies do not show consistent results. A study by Zhi 2011 found that the c.2101C>A genotype was associated with an increased risk of gastric cancer (OR = 8.42, 95% CI = 1.04-68.06) in Chinese males. The p.Gln701 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The p.Gln701Lys variant occurs in the 3rd last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 10, 2023	- -

Hereditary cancer-predisposing syndrome Benign:3

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. -
Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 27, 2015	- -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	Jun 29, 2021	- -

Lynch syndrome Uncertain:1 Benign:1

Likely benign, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Co-occurrence without CMMRD phenotype & MAF 0.01-1%. Multifactorial likelihood analysis posterior probability 0.001-0.049 -
Uncertain significance, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	May 14, 2015	- -

Lynch syndrome 1 Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Ding PR Lab, Sun Yat-sen University Cancer Center

-

- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

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

Apr 29, 2019

Variant summary: MLH1 c.2101C>A (p.Gln701Lys) results in a conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain of the encoded protein sequence that is necessary for interaction with PSM2 (Fan_2007). Three of five in-silico tools predict a benign effect of the variant on protein function. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0005 in 251174 control chromosomes (gnomAD and publication data), predominantly at a frequency of 0.0066 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 9 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Lynch Syndrome phenotype (0.00071), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. This variant has been reported in multiple sequencing studies among individuals of East Asian ancestry with a variety of cancers to include, Lynch Syndrome, biliary tract cancer and colon cancer (Zhi_2011, Talseth-Palmer_2016, Chan_2018, Kim_2017, Wardell_2018). Thus, these reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In addition, at-least one co-occurrence with the other potentially pathogenic variant (MLH1 c.208-1G>A) has been reported, providing supporting evidence for a benign role (Sheng_2008). A functional study demonstrated the variant to retain about 70% of its ability to interact with PMS2 (Fan_2007). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS (n=2), likely benign (n=2), and benign (n=2)). One expert panel (InSiGHT) has submitted clinical-significance assessment for this variant to ClinVar before 2014 and classified the variant as likely benign. As all of the evidence outlined above, spanning over a decade supports a non-pathogenic outcome, the variant was classified as benign. -

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

Feb 25, 2021

- -

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

Apr 29, 2022

- -

MLH1-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 27, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 27, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Pathogenic	0.45
Cadd	Benign	21
Dann	Benign	0.87
DEOGEN2	Uncertain	0.58	D;.;.;.;.;.
Eigen	Benign	-0.035
Eigen_PC	Benign	0.13
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.66	T;T;.;.;.;T
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.0071	T;T;T;T;T;T
MetaSVM	Uncertain	0.29	D
MutationAssessor	Benign	1.6	L;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.56	N;N;N;N;N;N
REVEL	Uncertain	0.52
Sift	Benign	0.90	T;D;T;T;T;T
Sift4G	Benign	0.92	T;T;T;T;T;T
Polyphen		0.10	B;.;.;.;.;.
Vest4		0.83
MVP		0.99
MPC		0.088
ClinPred		0.039	T
GERP RS		4.9
Varity_R		0.12
gMVP		0.63

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.026
dbscSNV1_RF	Benign	0.15
SpliceAI score (max)		0.020		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: rs63750114; hg19: chr3-37090506; COSMIC: COSV51617331; COSMIC: COSV51617331;