3-156548935-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007107.5(SSR3):c.329G>A(p.Arg110Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000112 in 1,613,508 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007107.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSR3 | NM_007107.5 | c.329G>A | p.Arg110Lys | missense_variant | Exon 3 of 5 | ENST00000265044.7 | NP_009038.1 | |
SSR3 | NM_001308197.2 | c.329G>A | p.Arg110Lys | missense_variant | Exon 3 of 5 | NP_001295126.1 | ||
SSR3 | NM_001308204.2 | c.173G>A | p.Arg58Lys | missense_variant | Exon 3 of 5 | NP_001295133.1 | ||
SSR3 | NM_001308205.2 | c.173G>A | p.Arg58Lys | missense_variant | Exon 3 of 5 | NP_001295134.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251032Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135714
GnomAD4 exome AF: 0.000116 AC: 170AN: 1461250Hom.: 1 Cov.: 35 AF XY: 0.000158 AC XY: 115AN XY: 726942
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74440
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 110 of the SSR3 protein (p.Arg110Lys). This variant is present in population databases (rs554757087, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SSR3-related conditions. ClinVar contains an entry for this variant (Variation ID: 2171056). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at