2-47800544-A-T

Position:

• chr2-47800544-A-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP3 BP4_Moderate BP6 BS1

The NM_000179.3(MSH6):​c.2561A>T​(p.Lys854Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00035 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00020 (0 hom.)
• Consequence: MSH6 NM_000179.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7 B:11 O:1
• Conservation: PhyloP100: 7.39

Genes affected

MSH6 (HGNC:7329): (mutS homolog 6) This gene encodes a member of the DNA mismatch repair MutS family. In E. coli, the MutS protein helps in the recognition of mismatched nucleotides prior to their repair. A highly conserved region of approximately 150 aa, called the Walker-A adenine nucleotide binding motif, exists in MutS homologs. The encoded protein heterodimerizes with MSH2 to form a mismatch recognition complex that functions as a bidirectional molecular switch that exchanges ADP and ATP as DNA mismatches are bound and dissociated. Mutations in this gene may be associated with hereditary nonpolyposis colon cancer, colorectal cancer, and endometrial cancer. Transcripts variants encoding different isoforms have been described. [provided by RefSeq, Jul 2013]

FBXO11 (HGNC:13590): (F-box protein 11) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. It can function as an arginine methyltransferase that symmetrically dimethylates arginine residues, and it acts as an adaptor protein to mediate the neddylation of p53, which leads to the suppression of p53 function. This gene is known to be down-regulated in melanocytes from patients with vitiligo, a skin disorder that results in depigmentation. Polymorphisms in this gene are associated with chronic otitis media with effusion and recurrent otitis media (COME/ROM), a hearing loss disorder, and the knockout of the homologous mouse gene results in the deaf mouse mutant Jeff (Jf), a single gene model of otitis media. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PP3: Multiple lines of computational evidence support a deleterious effect 6: AlphaMissense, BayesDel_noAF, M_CAP, MutationAssessor, PROVEAN, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• BP4: Computational evidence support a benign effect (MetaRNN=0.13576648).
• BP6: Variant 2-47800544-A-T is Benign according to our data. Variant chr2-47800544-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 89289.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=7, not_provided=1, Benign=3, Uncertain_significance=3}.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000355 (54/152276) while in subpopulation EAS AF= 0.00135 (7/5192). AF 95% confidence interval is 0.000632. There are 0 homozygotes in gnomad4. There are 27 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	Protein	UniProt
MSH6	NM_000179.3	c.2561A>T	p.Lys854Met	missense_variant	4/10	ENST00000234420.11	NP_000170.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSH6	ENST00000234420.11	c.2561A>T	p.Lys854Met	missense_variant	4/10	1	NM_000179.3	ENSP00000234420	P4

Frequencies

GnomAD3 genomes AF: 0.000355 AC: 54 AN: 152158 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000772

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000393 AC: 98 AN: 249296 Hom.: 0 AF XY: 0.000340 AC XY: 46 AN XY: 135256

Gnomad AFR exome AF: 0.000580

Gnomad AMR exome AF: 0.000261

Gnomad ASJ exome AF: 0.00190

Gnomad EAS exome AF: 0.00169

Gnomad SAS exome AF: 0.000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000124

Gnomad OTH exome AF: 0.000993

GnomAD4 exome AF: 0.000196 AC: 286 AN: 1461412 Hom.: 0 Cov.: 34 AF XY: 0.000184 AC XY: 134 AN XY: 727026

Gnomad4 AFR exome AF: 0.000719

Gnomad4 AMR exome AF: 0.000247

Gnomad4 ASJ exome AF: 0.00145

Gnomad4 EAS exome AF: 0.000731

Gnomad4 SAS exome AF: 0.000197

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000130

Gnomad4 OTH exome AF: 0.000265

GnomAD4 genome AF: 0.000355 AC: 54 AN: 152276 Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27 AN XY: 74470

Gnomad4 AFR AF: 0.000770

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000264 Hom.: 0

Bravo AF: 0.000510

ESP6500AA AF: 0.000228 AC: 1

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.000429 AC: 52

EpiCase AF: 0.000164

EpiControl AF: 0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:7 Benign:11 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1 Benign:4

Uncertain significance, no assertion criteria provided	clinical testing	True Health Diagnostics	Apr 27, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 06, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Apr 11, 2023	- -
Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	Jan 31, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 21, 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 Uncertain:1 Benign:2

Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 21, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 28, 2021	This variant is associated with the following publications: (PMID: 19389263, 14520694, 24728327, 16813607, 21153778, 23047549, 25637381, 15872200, 11470537, 26333163, 26898890, 25151137, 26530882, 23621914, 28767289, 29212164, 25479140, 29684080, 29368341, 28873162, 17531815) -

not specified Uncertain:1 Benign:1 Other:1

Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 06, 2021	Variant summary: MSH6 c.2561A>T (p.Lys854Met) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, core domain (IPR007696) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0004 in 249996 control chromosomes, predominantly at a frequency of 0.0017 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 12 fold of the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00014), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.2561A>T has been reported in the literature in individuals affected with cancer including pancreatic cancer, Lynch Syndrome, ovarian cancer and prostate cancer (Isaacsson Velho_2018, Shindo_2017, Grant_2015, Pal_2012, Suchy_2006, Hampel_2005, Peterlongo_2003, Ohmiya_2001). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In one study examining non-medullary thyroid cancer, the variant of interest was detected in only one of the two affected individuals from a single family (Yu_2015). At-least one co-occurrence with a pathogenic variant has been observed at our laboratory (BRCA2 c.1813delA, p.Ile605fsX9; internal testing), providing supporting evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant in a complete in vitro MMR (mismatch repair) activity (CIMRA) assay that was developed to quantify the functional activity of variants in MMR genes (Drost_2020). Ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments. Based on the predominant evidence supporting a neutral outcome as outlined above, the variant was re-classified as benign. -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 23, 2016	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: ClinVar: 5 VUS (including expert panel, no evidence supporting pathogenicity since expert classification) -

Colorectal cancer Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

Lynch syndrome 1 Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Ding PR Lab, Sun Yat-sen University Cancer Center

-

- -

MSH6-related disorder Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 16, 2024

The MSH6 c.2561A>T variant is predicted to result in the amino acid substitution p.Lys854Met. This variant has been reported in individuals with ovarian cancer (Pal et al. 2012, Table S1, PubMed ID: 23047549), colon cancer, melanoma (Ohmiya et al. 2001. PubMed ID: 11470537; Suchy et al. 2006. PubMed ID: 16813607), pancreatic cancer (Table S1, Shindo et al. 2017. PubMed ID: 28767289) and prostate cancer (Table S1, Isaacsson Velho et al. 2018. PubMed ID: 29368341), but in all cases was classified as a variant of uncertain significance. This variant was also identified in an individual from a cohort of healthy individuals (Table S1, Bodian et al. 2014. PubMed ID: 24728327) and has been reported with a frequency of 0.19% among individuals of Ashkenazi Jewish origin in the gnomAD database. In ClinVar, this variant has conflicting interpretations of pathogenicity including benign, likely benign, and uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89289/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Endometrial carcinoma;C1833477:Lynch syndrome 5;C5399763:Mismatch repair cancer syndrome 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Lynch syndrome 5 Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

Aug 22, 2023

- -

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

Mar 11, 2022

- -

Carcinoma of colon Benign:1

Likely benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MSH6 p.Lys854Met variant was identified in 6 of 6608 proband chromosomes (frequency: 0.0009) from individuals with colorectal, prostate, pancreatic and ovarian cancer and was present in 1 of 168 control chromosomes (frequency: 0.006) from healthy individuals (Ohmiya 2001, Peterlongo 2003, Pal 2012, Shindo 2017, Grant 2015, Isaacson-Velho). The variant was identified in dbSNP (rs34374438) as “with uncertain significance allele”, ClinVar (classified as uncertain significance by InSiGHT expert panel (2013), Ambry Genetics, GeneDx, and 8 other submitters and likely benign by Invitae and 1 other submitter) and UMD-LSDB (observed 1x). The variant was identified in control databases in 102 of 276,122 chromosomes at a frequency of 0.0004, 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: African in 12 of 23,992 chromosomes (freq: 0.0005), Other in 2 of 6446 chromosomes (freq: 0.0003), Latino in 10 of 34,336 chromosomes (freq: 0.0003), European in 13 of 125,966 chromosomes (freq: 0.0001), Ashkenazi Jewish in 24 of 10,104 chromosomes (freq: 0.002), East Asian in 31 of 18,844 chromosomes (freq: 0.002), and South Asian in 10 of 30,740 chromosomes (freq: 0.0003); it was not observed in the Finnish population. This variant was identified by our laboratory with a co-occurring, pathogenic variant in MSH2 (c.1786_1788del, p.Asn596del) increasing the likelihood the c.2561A>T variant may not have clinical significance. The p.Lys854 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume 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. -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.69
BayesDel_addAF	Uncertain	0.082	D
BayesDel_noAF	Pathogenic	0.33
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.81	.;.;D;T;.
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.96	.;D;D;D;D
M_CAP	Pathogenic	0.32	D
MetaRNN	Benign	0.14	T;T;T;T;T
MetaSVM	Pathogenic	0.82	D
MutationAssessor	Pathogenic	3.1	.;.;M;.;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-5.0	.;D;D;.;D
REVEL	Pathogenic	0.91
Sift	Uncertain	0.0020	.;D;D;.;D
Sift4G	Uncertain	0.0040	D;D;D;D;D
Polyphen		1.0	.;.;D;.;.
Vest4		0.55
MVP		0.95
ClinPred		0.11	T
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.89
gMVP		0.79

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: rs34374438; hg19: chr2-48027683; COSMIC: COSV105861230; COSMIC: COSV105861230;