rs28756982

Positions:

• chr14-75048398-C-T

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.1258G>A​(p.Val420Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,609,024 control chromosomes in the GnomAD database, including 181 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (13 hom., cov: 33)
  • Exomes 𝑓: 0.014 (168 hom.)
• Consequence: MLH3 NM_001040108.2 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10
• Conservation: PhyloP100: 0.942

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=0.001824379).
• BP6: Variant 14-75048398-C-T is Benign according to our data. Variant chr14-75048398-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 238243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-75048398-C-T is described in Lovd as [Benign]. Variant chr14-75048398-C-T is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0109 (1656/152240) while in subpopulation NFE AF= 0.0155 (1056/68006). AF 95% confidence interval is 0.0147. There are 13 homozygotes in gnomad4. There are 825 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1656 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH3	NM_001040108.2	c.1258G>A	p.Val420Ile	missense_variant	2/13	ENST00000355774.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH3	ENST00000355774.7	c.1258G>A	p.Val420Ile	missense_variant	2/13	5	NM_001040108.2	P1
MLH3	ENST00000380968.6	c.1258G>A	p.Val420Ile	missense_variant	2/12	1
MLH3	ENST00000556257.5	c.1258G>A	p.Val420Ile	missense_variant	2/7	5

Frequencies

GnomAD3 genomes AF: 0.0109 AC: 1657 AN: 152122 Hom.: 13 Cov.: 33

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.00574

GnomAD3 exomes AF: 0.0114 AC: 2811 AN: 246462 Hom.: 31 AF XY: 0.0112 AC XY: 1496 AN XY: 133112

Gnomad AFR exome AF: 0.00248

Gnomad AMR exome AF: 0.00182

Gnomad ASJ exome AF: 0.00841

Gnomad EAS exome AF: 0.0000550

Gnomad SAS exome AF: 0.00165

Gnomad FIN exome AF: 0.0345

Gnomad NFE exome AF: 0.0157

Gnomad OTH exome AF: 0.0115

GnomAD4 exome AF: 0.0140 AC: 20329 AN: 1456784 Hom.: 168 Cov.: 35 AF XY: 0.0136 AC XY: 9870 AN XY: 724338

Gnomad4 AFR exome AF: 0.00206

Gnomad4 AMR exome AF: 0.00197

Gnomad4 ASJ exome AF: 0.00862

Gnomad4 EAS exome AF: 0.0000757

Gnomad4 SAS exome AF: 0.00143

Gnomad4 FIN exome AF: 0.0339

Gnomad4 NFE exome AF: 0.0157

Gnomad4 OTH exome AF: 0.0104

GnomAD4 genome AF: 0.0109 AC: 1656 AN: 152240 Hom.: 13 Cov.: 33 AF XY: 0.0111 AC XY: 825 AN XY: 74430

Gnomad4 AFR AF: 0.00245

Gnomad4 AMR AF: 0.00216

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.00568

Alfa AF: 0.0136 Hom.: 3

Bravo AF: 0.00799

TwinsUK AF: 0.0181 AC: 67

ALSPAC AF: 0.0138 AC: 53

ESP6500AA AF: 0.00272 AC: 12

ESP6500EA AF: 0.0147 AC: 126

ExAC AF: 0.0115 AC: 1398

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.0126

EpiControl AF: 0.0127

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:3

Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 30, 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. -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Colorectal cancer, hereditary nonpolyposis, type 7 Benign:3

Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -

not provided Benign:3

Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MLH3 p.Val420Ile variant was identified in 4 of 174 proband chromosomes (frequency: 0.023) from individuals or families with Lynch Syndrome and was present in 2 of 180 control chromosomes (frequency: 0.01) from healthy individuals (Heinonen_2003_PMID: 12800209, Taylor_2006_PMID:16885347). The variant was also identified in dbSNP (ID: rs28756982) as likely benign, ClinVar (classified as benign by Invitae and likely benign by Illumina Clinical Service Laboratory), and LOVD 3.0 (classified as both uncertain significance and benign) databases. The variant was identified in control databases in 3222 of 277842 chromosomes (37 homozygous) at a frequency of 0.011597 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 (Finnish) in 847 of 25008 chromosomes (freq: 0.03387), European (non-Finnish) in 2026 of 127558 chromosomes (freq: 0.01588), Other in 87 of 7106 chromosomes (freq: 0.01224), Ashkenazi Jewish in 86 of 10164 chromosomes (freq: 0.008461), African in 64 of 24830 chromosomes (freq: 0.002578), Latino in 63 of 34392 chromosomes (freq: 0.001832), South Asian in 48 of 29030 chromosomes (freq: 0.001653), East Asian in 1 of 19754 chromosomes (freq: 0.000051). 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.Val420 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, and MutationTaster) do not suggest a high likelihood of impact to the protein; however, 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 03, 2023	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

MLH3-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 19, 2019

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

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.059
BayesDel_addAF	Benign	-0.56	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	2.4
DANN	Benign	0.52
DEOGEN2	Benign	0.084	T;.;.;T
Eigen	Benign	-1.1
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.0011	N
LIST_S2	Benign	0.31	T;T;T;.
MetaRNN	Benign	0.0018	T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-1.4	N;N;.;N
MutationTaster	Benign	1.0	N;N;N;N;N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.31	N;.;N;N
REVEL	Benign	0.18
Sift	Benign	0.45	T;.;T;T
Sift4G	Benign	0.63	T;T;T;T
Polyphen		0.0	B;B;.;B
Vest4		0.018
MPC		0.080
ClinPred		0.00068	T
GERP RS		3.2
Varity_R		0.028
gMVP		0.093

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: rs28756982; hg19: chr14-75515101; COSMIC: COSV104587306; COSMIC: COSV104587306;