7-26371904-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013322.3(SNX10):c.395C>T(p.Ala132Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,310 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A132A) has been classified as Likely benign.
Frequency
Consequence
NM_013322.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX10 | NM_013322.3 | c.395C>T | p.Ala132Val | missense_variant | Exon 6 of 7 | ENST00000338523.9 | NP_037454.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151852Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251280Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135816
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461458Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727032
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151852Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74170
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 132 of the SNX10 protein (p.Ala132Val). This variant is present in population databases (rs781164071, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SNX10-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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