Variant 12-20858879-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_019844.4(SLCO1B3):c.359+308C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 163,350 control chromosomes in the GnomAD database, including 46,366 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 42468 hom., cov: 31)

Exomes 𝑓: 0.82 ( 3898 hom. )

Consequence

SLCO1B3
NM_019844.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.29

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 links:

SLCO1B3-SLCO1B7 (HGNC:):

SLCO1B3-SLCO1B7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 12-20858879-C-T is Benign according to our data. Variant chr12-20858879-C-T is described in ClinVar as [Benign]. Clinvar id is 1234904.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-20858879-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SLCO1B3	NM_019844.4 linkuse as main transcript	c.359+308C>T	intron_variant	ENST00000381545.8	NP_062818.1
SLCO1B3-SLCO1B7	NM_001371097.1 linkuse as main transcript	c.359+308C>T	intron_variant		NP_001358026.1
SLCO1B3	NM_001349920.2 linkuse as main transcript	c.275+308C>T	intron_variant		NP_001336849.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SLCO1B3	ENST00000381545.8 linkuse as main transcript	c.359+308C>T	intron_variant	2	NM_019844.4	ENSP00000370956	P1	Q9NPD5-1
SLCO1B3	ENST00000261196.6 linkuse as main transcript	c.359+308C>T	intron_variant	1		ENSP00000261196	P1	Q9NPD5-1
SLCO1B3	ENST00000540853.5 linkuse as main transcript	c.359+308C>T	intron_variant	1		ENSP00000442000
SLCO1B3	ENST00000545880.1 linkuse as main transcript	n.212-7C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.725

AC:

110063

AN:

151756

Hom.:

42471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.859

Gnomad AMR

AF:

0.812

Gnomad ASJ

AF:

0.889

Gnomad EAS

AF:

0.720

Gnomad SAS

AF:

0.899

Gnomad FIN

AF:

0.747

Gnomad MID

AF:

0.883

Gnomad NFE

AF:

0.853

Gnomad OTH

AF:

0.779

GnomAD4 exome

AF:

0.819

AC:

9392

AN:

11472

Hom.:

3898

Cov.:

AF XY:

0.816

AC XY:

4963

AN XY:

6084

show subpopulations

Gnomad4 AFR exome

AF:

0.428

Gnomad4 AMR exome

AF:

0.801

Gnomad4 ASJ exome

AF:

0.897

Gnomad4 EAS exome

AF:

0.713

Gnomad4 SAS exome

AF:

0.884

Gnomad4 FIN exome

AF:

0.724

Gnomad4 NFE exome

AF:

0.843

Gnomad4 OTH exome

AF:

0.802

GnomAD4 genome

AF:

0.725

AC:

110088

AN:

151878

Hom.:

42468

Cov.:

AF XY:

0.724

AC XY:

53730

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.889

Gnomad4 EAS

AF:

0.720

Gnomad4 SAS

AF:

0.901

Gnomad4 FIN

AF:

0.747

Gnomad4 NFE

AF:

0.853

Gnomad4 OTH

AF:

0.778

Alfa

AF:

0.762

Hom.:

5681

Bravo

AF:

0.717

Asia WGS

AF:

0.759

AC:

2625

AN:

3464

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.4

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over