rs745685115
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.84+4G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 1,558,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
SLCO1B3
NM_019844.4 splice_region, intron
NM_019844.4 splice_region, intron
Scores
2
Splicing: ADA: 0.002667
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.50
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=-0.49).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLCO1B3 | NM_019844.4 | c.84+4G>C | splice_region_variant, intron_variant | Intron 3 of 15 | ENST00000381545.8 | NP_062818.1 | ||
| SLCO1B3-SLCO1B7 | NM_001371097.1 | c.84+4G>C | splice_region_variant, intron_variant | Intron 1 of 15 | NP_001358026.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLCO1B3 | ENST00000381545.8 | c.84+4G>C | splice_region_variant, intron_variant | Intron 3 of 15 | 2 | NM_019844.4 | ENSP00000370956.4 | |||
| SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.84+4G>C | splice_region_variant, intron_variant | Intron 1 of 15 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152120
Hom.:
Cov.:
33
Gnomad AFR
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000446 AC: 1AN: 224232 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
224232
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000135 AC: 19AN: 1406244Hom.: 0 Cov.: 24 AF XY: 0.0000172 AC XY: 12AN XY: 699702 show subpopulations
GnomAD4 exome
AF:
AC:
19
AN:
1406244
Hom.:
Cov.:
24
AF XY:
AC XY:
12
AN XY:
699702
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31928
American (AMR)
AF:
AC:
0
AN:
39606
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24852
East Asian (EAS)
AF:
AC:
0
AN:
38714
South Asian (SAS)
AF:
AC:
0
AN:
77390
European-Finnish (FIN)
AF:
AC:
0
AN:
51370
Middle Eastern (MID)
AF:
AC:
0
AN:
5548
European-Non Finnish (NFE)
AF:
AC:
19
AN:
1078876
Other (OTH)
AF:
AC:
0
AN:
57960
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.454
Heterozygous variant carriers
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Allele balance
GnomAD4 genome 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152120
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41426
American (AMR)
AF:
AC:
0
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68014
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
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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