12-20902672-G-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.51
Variant links:
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
SLCO1B3NM_019844.4 linkc.1865+1205G>C intron_variant Intron 15 of 15 ENST00000381545.8 NP_062818.1 Q9NPD5-1B3KP78
SLCO1B3-SLCO1B7NM_001371097.1 linkc.1865+1205G>C intron_variant Intron 13 of 15 NP_001358026.1
SLCO1B3NM_001349920.2 linkc.1781+1205G>C intron_variant Intron 13 of 13 NP_001336849.1
LOC124902894XM_047429949.1 linkc.-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
SLCO1B3ENST00000381545.8 linkc.1865+1205G>C intron_variant Intron 15 of 15 2 NM_019844.4 ENSP00000370956.4 Q9NPD5-1
SLCO1B3-SLCO1B7ENST00000540229.1 linkc.1865+1205G>C intron_variant Intron 13 of 15 2 ENSP00000441269.1 A0A0A6YYJ9
SLCO1B3ENST00000261196.6 linkc.1865+1205G>C intron_variant Intron 13 of 13 1 ENSP00000261196.2 Q9NPD5-1
SLCO1B3-SLCO1B7ENST00000381541.7 linkc.359+44101G>C intron_variant Intron 3 of 13 2 ENSP00000370952.3 F5H094-1

Frequencies

GnomAD3 genomes
AF:
0.715
AC:
108587
AN:
151918
Hom.:
43020
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.344
Gnomad AMI
AF:
0.898
Gnomad AMR
AF:
0.762
Gnomad ASJ
AF:
0.895
Gnomad EAS
AF:
0.761
Gnomad SAS
AF:
0.937
Gnomad FIN
AF:
0.770
Gnomad MID
AF:
0.870
Gnomad NFE
AF:
0.887
Gnomad OTH
AF:
0.760
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.714
AC:
108622
AN:
152036
Hom.:
43025
Cov.:
31
AF XY:
0.712
AC XY:
52935
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.344
Gnomad4 AMR
AF:
0.762
Gnomad4 ASJ
AF:
0.895
Gnomad4 EAS
AF:
0.762
Gnomad4 SAS
AF:
0.938
Gnomad4 FIN
AF:
0.770
Gnomad4 NFE
AF:
0.887
Gnomad4 OTH
AF:
0.763
Alfa
AF:
0.699
Hom.:
2498
Bravo
AF:
0.698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.14
DANN
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4762803; hg19: chr12-21055606; API