12-20815807-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_019844.4(SLCO1B3):c.69C>T(p.Arg23Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000697 in 1,591,432 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_019844.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.69C>T | p.Arg23Arg | synonymous_variant | Exon 3 of 16 | 2 | NM_019844.4 | ENSP00000370956.4 | ||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.69C>T | p.Arg23Arg | synonymous_variant | Exon 1 of 16 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes AF: 0.00397 AC: 604AN: 152038Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00103 AC: 244AN: 237710Hom.: 1 AF XY: 0.000628 AC XY: 81AN XY: 128894
GnomAD4 exome AF: 0.000350 AC: 504AN: 1439276Hom.: 5 Cov.: 28 AF XY: 0.000260 AC XY: 186AN XY: 715664
GnomAD4 genome AF: 0.00398 AC: 606AN: 152156Hom.: 4 Cov.: 33 AF XY: 0.00399 AC XY: 297AN XY: 74366
ClinVar
Submissions by phenotype
Rotor syndrome Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at