6-31761582-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_172166.4(MSH5):c.2148A>G(p.Gln716Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,613,718 control chromosomes in the GnomAD database, including 106,430 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_172166.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSH5 | NM_172166.4 | c.2148A>G | p.Gln716Gln | synonymous_variant | Exon 22 of 25 | ENST00000375750.9 | NP_751898.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH5 | ENST00000375750.9 | c.2148A>G | p.Gln716Gln | synonymous_variant | Exon 22 of 25 | 1 | NM_172166.4 | ENSP00000364903.3 | ||
MSH5-SAPCD1 | ENST00000493662.6 | n.2199A>G | non_coding_transcript_exon_variant | Exon 22 of 29 | 1 | ENSP00000417871.2 |
Frequencies
GnomAD3 genomes AF: 0.433 AC: 65835AN: 151992Hom.: 15848 Cov.: 33
GnomAD3 exomes AF: 0.382 AC: 95769AN: 250692Hom.: 19610 AF XY: 0.379 AC XY: 51357AN XY: 135678
GnomAD4 exome AF: 0.344 AC: 503039AN: 1461606Hom.: 90547 Cov.: 66 AF XY: 0.346 AC XY: 251597AN XY: 727108
GnomAD4 genome AF: 0.433 AC: 65921AN: 152112Hom.: 15883 Cov.: 33 AF XY: 0.437 AC XY: 32523AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
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: Frequency -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at