13-103046190-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000452.3(SLC10A2):c.990G>A(p.Thr330Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000452.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251180Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135772
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461564Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727094
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
SLC10A2-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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at