rs28756986

chr14-75047786-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001040108.2(MLH3):c.1870G>C(p.Glu624Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00964 in 1,614,018 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0075 (6 hom., cov: 33)
  • Exomes 𝑓: 0.0099 (89 hom.)
• Consequence: MLH3 NM_001040108.2 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1 B:9
• Conservation: PhyloP100: 1.23

Genes affected

MLH3 (HGNC:7128): (mutL homolog 3) This gene is a member of the MutL-homolog (MLH) family of DNA mismatch repair (MMR) genes. MLH genes are implicated in maintaining genomic integrity during DNA replication and after meiotic recombination. The protein encoded by this gene functions as a heterodimer with other family members. Somatic mutations in this gene frequently occur in tumors exhibiting microsatellite instability, and germline mutations have been linked to hereditary nonpolyposis colorectal cancer type 7 (HNPCC7). Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0042276084).
• BP6: Variant 14-75047786-C-G is Benign according to our data. Variant chr14-75047786-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 5560.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-75047786-C-G is described in Lovd as [Pathogenic]. Variant chr14-75047786-C-G is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00745 (1135/152320) while in subpopulation NFE AF= 0.0121 (823/68032). AF 95% confidence interval is 0.0114. There are 6 homozygotes in gnomad4. There are 528 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd at 1134 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH3	NM_001040108.2	c.1870G>C	p.Glu624Gln	missense_variant	2/13	ENST00000355774.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH3	ENST00000355774.7	c.1870G>C	p.Glu624Gln	missense_variant	2/13	5	NM_001040108.2	P1
MLH3	ENST00000380968.6	c.1870G>C	p.Glu624Gln	missense_variant	2/12	1
MLH3	ENST00000556257.5	c.1870G>C	p.Glu624Gln	missense_variant	2/7	5

Frequencies

GnomAD3 genomes AF: 0.00745 AC: 1134 AN: 152202 Hom.: 6 Cov.: 33

Gnomad AFR AF: 0.00222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00772

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.00719

GnomAD3 exomes AF: 0.00716 AC: 1799 AN: 251246 Hom.: 8 AF XY: 0.00712 AC XY: 967 AN XY: 135764

Gnomad AFR exome AF: 0.00222

Gnomad AMR exome AF: 0.00582

Gnomad ASJ exome AF: 0.00377

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00173

Gnomad FIN exome AF: 0.00804

Gnomad NFE exome AF: 0.0111

Gnomad OTH exome AF: 0.00636

GnomAD4 exome AF: 0.00987 AC: 14420 AN: 1461698 Hom.: 89 Cov.: 35 AF XY: 0.00959 AC XY: 6976 AN XY: 727156

Gnomad4 AFR exome AF: 0.00185

Gnomad4 AMR exome AF: 0.00575

Gnomad4 ASJ exome AF: 0.00394

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00167

Gnomad4 FIN exome AF: 0.00953

Gnomad4 NFE exome AF: 0.0115

Gnomad4 OTH exome AF: 0.00894

GnomAD4 genome AF: 0.00745 AC: 1135 AN: 152320 Hom.: 6 Cov.: 33 AF XY: 0.00709 AC XY: 528 AN XY: 74492

Gnomad4 AFR AF: 0.00221

Gnomad4 AMR AF: 0.00771

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00641

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.00712

Alfa AF: 0.0109 Hom.: 9

Bravo AF: 0.00689

TwinsUK AF: 0.0146 AC: 54

ALSPAC AF: 0.0148 AC: 57

ESP6500AA AF: 0.00295 AC: 13

ESP6500EA AF: 0.0121 AC: 104

ExAC AF: 0.00728 AC: 884

Asia WGS AF: 0.00173 AC: 6 AN: 3478

EpiCase AF: 0.0100

EpiControl AF: 0.00931

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1 Benign:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 7 Uncertain:1 Benign:3

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 28, 2024	- -
Uncertain significance, no assertion criteria provided	literature only	OMIM	Apr 01, 2009	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Likely benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

not specified Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 01, 2020	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. -

not provided Benign:3

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MLH3 p.Glu624Gln variant was identified in 7 of 1036 proband chromosomes (frequency: 0.00676) from individuals or families with suspected Lynch syndrome or colorectal cancer (Wu_2001_PMID: 11586295, Liu_2003_PMID: 12702580, Rohlin_2017_PMID: 27696107, & Hienonen_2003_PMID: 12800209). The variant was also identified in the following databases: dbSNP (ID: rs28756986) as “With Uncertain significance allele”, ClinVar (classified as benign by Invitae with the associated phenotype of Hereditary nonpolyposis colorectal cancer type 7/MLH3-Related Lynch Syndrome; and uncertain significance by OMIM), and LOVD 3.0 (multiple entries with classifications of VUS, likely benign, and pathogenic). The variant was not identified in the Cosmic database. The variant was identified in control databases in 2120 of 282638 chromosomes (11 homozygous) at a frequency of 0.007501 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 1516 of 129054 chromosomes (freq: 0.01175), European (Finnish) in 201 of 25108 chromosomes (freq: 0.008005), Other in 49 of 7218 chromosomes (freq: 0.006789), Latino in 210 of 35396 chromosomes (freq: 0.005933), Ashkenazi Jewish in 39 of 10362 chromosomes (freq: 0.003764), African in 51 of 24968 chromosomes (freq: 0.002043), South Asian in 53 of 30584 chromosomes (freq: 0.001733) and East Asian in 1 of 19948 chromosomes (freq: 0.00005). To clarify the role of the p.E624Q, in vitro functional studies were conducted transfecting wildtype and mutant MLH3 into HEK293T cells which showed no difference in protein expression, stability, localization or interaction with wildtype MLH1 (Ou_2009_PMID: 19156873). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, and GeneSplicer) do not predict a difference in splicing. The p.Glu624 residue is conserved in mammals but not in more distantly related organisms, however four out of five computational analyses (SIFT, AlignGVGD, BLOSUM, and MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. 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	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 28, 2023	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.16
Cadd	Benign	20
Dann	Uncertain	0.99
DEOGEN2	Benign	0.11	T;.;.;T
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.32
FATHMM_MKL	Benign	0.62	D
LIST_S2	Uncertain	0.89	D;D;D;.
MetaRNN	Benign	0.0042	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	M;M;.;M
MutationTaster	Benign	1.0	D;N;N;N;N
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-1.4	N;.;N;N
REVEL	Benign	0.19
Sift	Benign	0.043	D;.;T;D
Sift4G	Benign	0.10	T;T;T;T
Polyphen		0.99	D;D;.;D
Vest4		0.11
MVP		0.64
MPC		0.11
ClinPred		0.014	T
GERP RS		3.9
Varity_R		0.17
gMVP		0.38

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: rs28756986; hg19: chr14-75514489; COSMIC: COSV53156471; COSMIC: COSV53156471;