rs61752722

Positions:

• chr14-75047231-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_001040108.2(MLH3):​c.2425A>G​(p.Met809Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,614,142 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0025 (15 hom.)
• Consequence: MLH3 NM_001040108.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:8
• Conservation: PhyloP100: -4.28

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.003596425).
• BP6: Variant 14-75047231-T-C is Benign according to our data. Variant chr14-75047231-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 416460.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=5, Uncertain_significance=1}. Variant chr14-75047231-T-C is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00198 (301/152334) while in subpopulation NFE AF= 0.003 (204/68022). AF 95% confidence interval is 0.00266. There are 0 homozygotes in gnomad4. There are 135 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 301 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH3	NM_001040108.2	c.2425A>G	p.Met809Val	missense_variant	2/13	ENST00000355774.7	NP_001035197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH3	ENST00000355774.7	c.2425A>G	p.Met809Val	missense_variant	2/13	5	NM_001040108.2	ENSP00000348020	P1
MLH3	ENST00000380968.6	c.2425A>G	p.Met809Val	missense_variant	2/12	1		ENSP00000370355
MLH3	ENST00000556257.5	c.2425A>G	p.Met809Val	missense_variant	2/7	5		ENSP00000451540
MLH3	ENST00000555671.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.00198 AC: 301 AN: 152216 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000434

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.00137

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00300

Gnomad OTH AF: 0.00287

GnomAD3 exomes AF: 0.00184 AC: 463 AN: 251394 Hom.: 2 AF XY: 0.00201 AC XY: 273 AN XY: 135874

Gnomad AFR exome AF: 0.000369

Gnomad AMR exome AF: 0.000463

Gnomad ASJ exome AF: 0.00268

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00245

Gnomad FIN exome AF: 0.000971

Gnomad NFE exome AF: 0.00268

Gnomad OTH exome AF: 0.00196

GnomAD4 exome AF: 0.00254 AC: 3711 AN: 1461808 Hom.: 15 Cov.: 35 AF XY: 0.00261 AC XY: 1896 AN XY: 727200

Gnomad4 AFR exome AF: 0.000388

Gnomad4 AMR exome AF: 0.000693

Gnomad4 ASJ exome AF: 0.00318

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00265

Gnomad4 FIN exome AF: 0.00114

Gnomad4 NFE exome AF: 0.00284

Gnomad4 OTH exome AF: 0.00189

GnomAD4 genome AF: 0.00198 AC: 301 AN: 152334 Hom.: 0 Cov.: 33 AF XY: 0.00181 AC XY: 135 AN XY: 74496

Gnomad4 AFR AF: 0.000433

Gnomad4 AMR AF: 0.00137

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00291

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00300

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00290 Hom.: 3

Bravo AF: 0.00182

TwinsUK AF: 0.00297 AC: 11

ALSPAC AF: 0.00156 AC: 6

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.00267 AC: 23

ExAC AF: 0.00195 AC: 237

Asia WGS AF: 0.00144 AC: 5 AN: 3476

EpiCase AF: 0.00371

EpiControl AF: 0.00296

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:8

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 7 Uncertain:1 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Uncertain significance, 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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 01, 2020	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. -

not provided Benign:2

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MLH3 p.Met809Val variant was not identified in Cosmic but was identified in dbSNP (ID: rs61752722), LOVD 3.0 and ClinVar (classified as likely benign for MLH3-related Lynch Syndrome by Invitae). The variant was identified in control databases in 527 of 282794 chromosomes (2 homozygous) at a frequency of 0.001864 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 357 of 129132 chromosomes (freq: 0.002765), Ashkenazi Jewish in 28 of 10368 chromosomes (freq: 0.002701), South Asian in 75 of 30610 chromosomes (freq: 0.00245), Other in 14 of 7222 chromosomes (freq: 0.001939), European (Finnish) in 24 of 25106 chromosomes (freq: 0.000956), Latino in 17 of 35440 chromosomes (freq: 0.00048), African in 11 of 24962 chromosomes (freq: 0.000441), and East Asian in 1 of 19954 chromosomes (freq: 0.00005). This variant has been reported with an overall frequency of 0.009 in multiple studies analyzing germline mutations in colorectal cancer cases, however it has been suggested to be benign (Hienonen_2003_PMID: 12800209; Lefevre_2012_PMID: 22875147; Vargas-Parra_2017_PMID: 28577310). The p.Met809 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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. -

Lynch syndrome 1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Human Genetics Bochum, Ruhr University Bochum

Oct 24, 2022

ACMG criteria used to clasify this variant: BS1, BS2 -

Malignant tumor of breast Benign:1

Likely benign, no assertion criteria provided

clinical testing

Center of Medical Genetics and Primary Health Care

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.59	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.0010
DANN	Benign	0.18
DEOGEN2	Benign	0.079	T;.;.;T
Eigen	Benign	-2.0
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.018	N
LIST_S2	Benign	0.43	T;T;T;.
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.0036	T;T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.0	N;N;.;N
MutationTaster	Benign	1.0	N;N;N;N;N
PrimateAI	Benign	0.20	T
PROVEAN	Benign	0.33	N;.;N;N
REVEL	Benign	0.23
Sift	Benign	1.0	T;.;T;T
Sift4G	Benign	0.62	T;T;T;T
Polyphen		0.0	B;B;.;B
Vest4		0.032
MVP		0.31
MPC		0.10
ClinPred		0.0033	T
GERP RS		-12
Varity_R		0.039
gMVP		0.16

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: rs61752722; hg19: chr14-75513934; COSMIC: COSV99470867; COSMIC: COSV99470867;