Variant 12-20815731-GTTTA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_019844.4(SLCO1B3):c.-7_-4delTTTA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,547,798 control chromosomes in the GnomAD database, including 55,692 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4630 hom., cov: 24)

Exomes 𝑓: 0.26 ( 51062 hom. )

Consequence

SLCO1B3
NM_019844.4 5_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 3.21

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: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]

SLCO1B3-SLCO1B7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-20815731-GTTTA-G is Benign according to our data. Variant chr12-20815731-GTTTA-G is described in ClinVar as [Benign]. Clinvar id is 440287.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO1B3	NM_019844.4 linkuse as main transcript	c.-7_-4delTTTA		5_prime_UTR_variant	3/16	ENST00000381545.8	NP_062818.1	Q9NPD5-1B3KP78
SLCO1B3-SLCO1B7	NM_001371097.1 linkuse as main transcript	c.-7_-4delTTTA		5_prime_UTR_variant	1/16		NP_001358026.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO1B3	ENST00000381545.8 linkuse as main transcript	c.-7_-4delTTTA		5_prime_UTR_variant	3/16	2	NM_019844.4	ENSP00000370956.4		Q9NPD5-1
SLCO1B3-SLCO1B7	ENST00000540229.1 linkuse as main transcript	c.-7_-4delTTTA		5_prime_UTR_variant	1/16	2		ENSP00000441269.1		A0A0A6YYJ9

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35586

AN:

151966

Hom.:

4631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.154

AC:

31904

AN:

207762

Hom.:

3802

AF XY:

0.162

AC XY:

18305

AN XY:

112928

show subpopulations

Gnomad AFR exome

AF:

0.0802

Gnomad AMR exome

AF:

0.0759

Gnomad ASJ exome

AF:

0.159

Gnomad EAS exome

AF:

0.0846

Gnomad SAS exome

AF:

0.0941

Gnomad FIN exome

AF:

0.163

Gnomad NFE exome

AF:

0.215

Gnomad OTH exome

AF:

0.152

GnomAD4 exome

AF:

0.261

AC:

364166

AN:

1395712

Hom.:

51062

AF XY:

0.259

AC XY:

179963

AN XY:

694372

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.150

Gnomad4 ASJ exome

AF:

0.241

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.284

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.234

AC:

35612

AN:

152086

Hom.:

4630

Cov.:

AF XY:

0.231

AC XY:

17146

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.263

Gnomad4 EAS

AF:

0.170

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.106

Hom.:

449

Asia WGS

AF:

0.162

AC:

558

AN:

3466

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Rotor syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 30, 2023

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.29

Position offset: 5

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