chr14-69776375-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003049.4(SLC10A1):c.957G>A(p.Met319Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,613,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M319T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003049.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000587 AC: 89AN: 151622Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000184 AC: 46AN: 250654Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135548
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461576Hom.: 0 Cov.: 30 AF XY: 0.000103 AC XY: 75AN XY: 727086
GnomAD4 genome AF: 0.000600 AC: 91AN: 151738Hom.: 0 Cov.: 32 AF XY: 0.000634 AC XY: 47AN XY: 74182
ClinVar
Submissions by phenotype
not provided Uncertain:1
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SLC10A1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at