12-20902672-G-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019844.4(SLCO1B3):c.1865+1205G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,036 control chromosomes in the GnomAD database, including 43,025 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.71 ( 43025 hom., cov: 31)
Consequence
SLCO1B3
NM_019844.4 intron
NM_019844.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.51
Genes affected
SLCO1B3 (HGNC:10961): (solute carrier organic anion transporter family member 1B3) This gene encodes a liver-specific member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of endogenous and xenobiotic compounds and plays a critical role in bile acid and bilirubin transport. Mutations in this gene are a cause of Rotor type hyperbilirubinemia. Alternative splicing of this gene and the use of alternative promoters results in transcript variants encoding different isoforms that differ in their tissue specificity. [provided by RefSeq, Mar 2017]
SLCO1B3-SLCO1B7 (HGNC:54403): (SLCO1B3-SLCO1B7 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring SLCO1B3 (solute carrier organic anion transporter family member 1B3) and SLCO1B7 (solute carrier organic anion transporter family member 1B7 (putative)) genes on chromosome 12. The readthrough transcript encodes a protein that shares sequence identity with both the upstream and downstream genes. [provided by RefSeq, Jun 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.06).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.1865+1205G>C | intron_variant | Intron 15 of 15 | ENST00000381545.8 | NP_062818.1 | ||
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.1865+1205G>C | intron_variant | Intron 13 of 15 | NP_001358026.1 | |||
SLCO1B3 | NM_001349920.2 | c.1781+1205G>C | intron_variant | Intron 13 of 13 | NP_001336849.1 | |||
LOC124902894 | XM_047429949.1 | c.-58+1205G>C | intron_variant | Intron 1 of 9 | XP_047285905.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.1865+1205G>C | intron_variant | Intron 15 of 15 | 2 | NM_019844.4 | ENSP00000370956.4 | |||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.1865+1205G>C | intron_variant | Intron 13 of 15 | 2 | ENSP00000441269.1 | ||||
SLCO1B3 | ENST00000261196.6 | c.1865+1205G>C | intron_variant | Intron 13 of 13 | 1 | ENSP00000261196.2 | ||||
SLCO1B3-SLCO1B7 | ENST00000381541.7 | c.359+44101G>C | intron_variant | Intron 3 of 13 | 2 | ENSP00000370952.3 |
Frequencies
GnomAD3 genomes AF: 0.715 AC: 108587AN: 151918Hom.: 43020 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.714 AC: 108622AN: 152036Hom.: 43025 Cov.: 31 AF XY: 0.712 AC XY: 52935AN XY: 74300
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at