2-47783075-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000652107.1(MSH6):​c.-37-7852C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 862,978 control chromosomes in the GnomAD database, including 4,218 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

Frequency

Genomes: 𝑓 0.073 ( 573 hom., cov: 33)
Exomes 𝑓: 0.094 ( 3645 hom. )

Consequence

MSH6
ENST00000652107.1 intron

Scores

2

Clinical Significance

Benign reviewed by expert panel B:4

Conservation

PhyloP100: -0.469
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 2-47783075-C-T is Benign according to our data. Variant chr2-47783075-C-T is described in ClinVar as [Benign]. Clinvar id is 89158.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47783075-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MSH6ENST00000652107.1 linkuse as main transcriptc.-37-7852C>T intron_variant ENSP00000498629
MSH6ENST00000445503.5 linkuse as main transcript upstream_gene_variant 1 ENSP00000405294

Frequencies

GnomAD3 genomes
AF:
0.0726
AC:
11022
AN:
151740
Hom.:
573
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0202
Gnomad AMI
AF:
0.0450
Gnomad AMR
AF:
0.0490
Gnomad ASJ
AF:
0.0366
Gnomad EAS
AF:
0.000583
Gnomad SAS
AF:
0.0135
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.109
Gnomad OTH
AF:
0.0729
GnomAD4 exome
AF:
0.0935
AC:
66524
AN:
711130
Hom.:
3645
Cov.:
9
AF XY:
0.0905
AC XY:
32500
AN XY:
359156
show subpopulations
Gnomad4 AFR exome
AF:
0.0167
Gnomad4 AMR exome
AF:
0.0476
Gnomad4 ASJ exome
AF:
0.0406
Gnomad4 EAS exome
AF:
0.000160
Gnomad4 SAS exome
AF:
0.0191
Gnomad4 FIN exome
AF:
0.147
Gnomad4 NFE exome
AF:
0.107
Gnomad4 OTH exome
AF:
0.0776
GnomAD4 genome
AF:
0.0726
AC:
11024
AN:
151848
Hom.:
573
Cov.:
33
AF XY:
0.0721
AC XY:
5352
AN XY:
74202
show subpopulations
Gnomad4 AFR
AF:
0.0202
Gnomad4 AMR
AF:
0.0489
Gnomad4 ASJ
AF:
0.0366
Gnomad4 EAS
AF:
0.000584
Gnomad4 SAS
AF:
0.0139
Gnomad4 FIN
AF:
0.157
Gnomad4 NFE
AF:
0.109
Gnomad4 OTH
AF:
0.0716
Alfa
AF:
0.0874
Hom.:
169
Bravo
AF:
0.0621

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Lynch syndrome Benign:2
Benign, reviewed by expert panelresearchInternational Society for Gastrointestinal Hereditary Tumours (InSiGHT)Sep 05, 2013MAF >1% -
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 23, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
7.7
DANN
Benign
0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41540312; hg19: chr2-48010214; API