Variant chr12-20815894-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.84+72C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 844,514 control chromosomes in the GnomAD database, including 385,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.90 ( 63027 hom., cov: 32)

Exomes 𝑓: 0.96 ( 322416 hom. )

Consequence

SLCO1B3
NM_019844.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.447

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=-0.83).

BP6

Variant 12-20815894-C-T is Benign according to our data. Variant chr12-20815894-C-T is described in ClinVar as [Benign]. Clinvar id is 1274436.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO1B3	NM_019844.4 linkuse as main transcript	c.84+72C>T		intron_variant		ENST00000381545.8
SLCO1B3-SLCO1B7	NM_001371097.1 linkuse as main transcript	c.84+72C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
SLCO1B3	ENST00000381545.8 linkuse as main transcript	c.84+72C>T	intron_variant	2	NM_019844.4	P1	Q9NPD5-1
SLCO1B3	ENST00000261196.6 linkuse as main transcript	c.84+72C>T	intron_variant	1		P1	Q9NPD5-1
SLCO1B3	ENST00000540853.5 linkuse as main transcript	c.84+72C>T	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.904

AC:

137499

AN:

152122

Hom.:

62982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.980

Gnomad AMR

AF:

0.954

Gnomad ASJ

AF:

0.972

Gnomad EAS

AF:

0.992

Gnomad SAS

AF:

0.946

Gnomad FIN

AF:

0.967

Gnomad MID

AF:

0.915

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.917

GnomAD4 exome

AF:

0.964

AC:

667434

AN:

692274

Hom.:

322416

AF XY:

0.964

AC XY:

349219

AN XY:

362188

show subpopulations

Gnomad4 AFR exome

AF:

0.715

Gnomad4 AMR exome

AF:

0.965

Gnomad4 ASJ exome

AF:

0.970

Gnomad4 EAS exome

AF:

0.993

Gnomad4 SAS exome

AF:

0.954

Gnomad4 FIN exome

AF:

0.969

Gnomad4 NFE exome

AF:

0.972

Gnomad4 OTH exome

AF:

0.953

GnomAD4 genome

AF:

0.904

AC:

137598

AN:

152240

Hom.:

63027

Cov.:

AF XY:

0.907

AC XY:

67479

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.734

Gnomad4 AMR

AF:

0.954

Gnomad4 ASJ

AF:

0.972

Gnomad4 EAS

AF:

0.992

Gnomad4 SAS

AF:

0.947

Gnomad4 FIN

AF:

0.967

Gnomad4 NFE

AF:

0.972

Gnomad4 OTH

AF:

0.918

Alfa

AF:

0.931

Hom.:

19257

Bravo

AF:

0.895

Asia WGS

AF:

0.956

AC:

3303

AN:

3458

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.1

DANN

Benign

0.50

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.

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