rs78862986
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019844.4(SLCO1B3):c.1866-23C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000287 in 1,392,434 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000029 ( 0 hom. )
Consequence
SLCO1B3
NM_019844.4 intron
NM_019844.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.397
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLCO1B3 | NM_019844.4 | c.1866-23C>G | intron_variant | Intron 15 of 15 | ENST00000381545.8 | NP_062818.1 | ||
| SLCO1B3-SLCO1B7 | NM_001371097.1 | c.1865+14514C>G | intron_variant | Intron 13 of 15 | NP_001358026.1 | |||
| SLCO1B3 | NM_001349920.2 | c.1782-23C>G | intron_variant | Intron 13 of 13 | NP_001336849.1 | |||
| LOC124902894 | XM_047429949.1 | c.-58+14514C>G | 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.1866-23C>G | intron_variant | Intron 15 of 15 | 2 | NM_019844.4 | ENSP00000370956.4 | |||
| SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.1865+14514C>G | intron_variant | Intron 13 of 15 | 2 | ENSP00000441269.1 | ||||
| SLCO1B3 | ENST00000261196.6 | c.1866-23C>G | intron_variant | Intron 13 of 13 | 1 | ENSP00000261196.2 | ||||
| SLCO1B3-SLCO1B7 | ENST00000381541.7 | c.359+57410C>G | intron_variant | Intron 3 of 13 | 2 | ENSP00000370952.3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000287 AC: 4AN: 1392434Hom.: 0 Cov.: 27 AF XY: 0.00000433 AC XY: 3AN XY: 692408 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1392434
Hom.:
Cov.:
27
AF XY:
AC XY:
3
AN XY:
692408
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30528
American (AMR)
AF:
AC:
0
AN:
35232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23860
East Asian (EAS)
AF:
AC:
0
AN:
39020
South Asian (SAS)
AF:
AC:
0
AN:
79114
European-Finnish (FIN)
AF:
AC:
0
AN:
51962
Middle Eastern (MID)
AF:
AC:
0
AN:
4932
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1070310
Other (OTH)
AF:
AC:
0
AN:
57476
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
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1
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2
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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