12-20815821-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019844.4(SLCO1B3):āc.83A>Gā(p.Lys28Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000191 in 1,572,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_019844.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.83A>G | p.Lys28Arg | missense_variant, splice_region_variant | Exon 3 of 16 | ENST00000381545.8 | NP_062818.1 | |
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.83A>G | p.Lys28Arg | missense_variant, splice_region_variant | Exon 1 of 16 | NP_001358026.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.83A>G | p.Lys28Arg | missense_variant, splice_region_variant | Exon 3 of 16 | 2 | NM_019844.4 | ENSP00000370956.4 | ||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.83A>G | p.Lys28Arg | missense_variant, splice_region_variant | Exon 1 of 16 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD4 exome AF: 7.04e-7 AC: 1AN: 1419706Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 706144
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74502
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at