rs369971640

Variant names:

• chr2-47798594-C-A
• rs369971640
• NM_000179.3:c.628-17C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-47798594-C-A
• chr2-47798594-C-G
• chr2-47798594-C-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_000179.3(MSH6):​c.628-17C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000268 in 1,606,224 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00028 (3 hom.)
• Consequence: MSH6 NM_000179.3 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: 0.0760
• Publications: 0 publications found

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]

FBXO11 Gene-Disease associations (from GenCC):

• intellectual developmental disorder with dysmorphic facies and behavioral abnormalities

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 2-47798594-C-A is Benign according to our data. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47798594-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 381343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000184 (28/152304) while in subpopulation SAS AF = 0.0056 (27/4820). AF 95% confidence interval is 0.00395. There are 0 homozygotes in GnomAd4. There are 25 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSH6	NM_000179.3	c.628-17C>A		intron_variant	Intron 3 of 9	ENST00000234420.11	NP_000170.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSH6	ENST00000234420.11	c.628-17C>A		intron_variant	Intron 3 of 9	1	NM_000179.3	ENSP00000234420.5

Frequencies

GnomAD3 genomes AF: 0.000184 AC: 28 AN: 152186 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000509 AC: 123 AN: 241732 AF XY: 0.000677

Gnomad AFR exome AF: 0.0000633

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000277 AC: 403 AN: 1453920 Hom.: 3 Cov.: 33 AF XY: 0.000399 AC XY: 289 AN XY: 723454

African (AFR) AF: 0.0000598 AC: 2 AN: 33450

American (AMR) AF: 0.00 AC: 0 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00452 AC: 389 AN: 86100

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46428

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5402

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111708

Other (OTH) AF: 0.000166 AC: 10 AN: 60308

GnomAD4 genome AF: 0.000184 AC: 28 AN: 152304 Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25 AN XY: 74480

African (AFR) AF: 0.0000241 AC: 1 AN: 41570

American (AMR) AF: 0.00 AC: 0 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68024

Other (OTH) AF: 0.00 AC: 0 AN: 2116

Alfa AF: 0.0000854 Hom.: 0

Bravo AF: 0.0000416

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

May 19, 2016

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:2

May 29, 2016

Color Diagnostics, LLC DBA Color Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 03, 2015

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Lynch syndrome 5 Benign:1

Dec 19, 2024

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726]. This variant has been observed in conjunction with multiple pathogenic variants, reducing the likelihood this variant itself is pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		0.076
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs369971640; hg19: chr2-48025733;