Variant 12-20815710-AATATTCACTTGGTATCTG-A 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.-28_-11del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,469,848 control chromosomes in the GnomAD database, including 54,843 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4628 hom., cov: 23)

Exomes 𝑓: 0.27 ( 50215 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: 0.607

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 -16 ACMG points.

BP6

Variant 12-20815710-AATATTCACTTGGTATCTG-A is Benign according to our data. Variant chr12-20815710-AATATTCACTTGGTATCTG-A is described in ClinVar as [Benign]. Clinvar id is 993345.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	UniProt
SLCO1B3	NM_019844.4 linkuse as main transcript	c.-28_-11del		5_prime_UTR_variant	3/16	ENST00000381545.8
SLCO1B3-SLCO1B7	NM_001371097.1 linkuse as main transcript	c.-28_-11del		5_prime_UTR_variant	1/16

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO1B3	ENST00000381545.8 linkuse as main transcript	c.-28_-11del	5_prime_UTR_variant	3/16	2	NM_019844.4	P1	Q9NPD5-1
SLCO1B3	ENST00000261196.6 linkuse as main transcript	c.-28_-11del	5_prime_UTR_variant	1/14	1		P1	Q9NPD5-1
SLCO1B3	ENST00000540853.5 linkuse as main transcript	c.-28_-11del	5_prime_UTR_variant	2/8	1

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35565

AN:

152042

Hom.:

4629

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:

0.169

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.140

AC:

29724

AN:

212094

Hom.:

3670

AF XY:

0.149

AC XY:

17141

AN XY:

115188

show subpopulations

Gnomad AFR exome

AF:

0.0751

Gnomad AMR exome

AF:

0.0686

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.0765

Gnomad SAS exome

AF:

0.0867

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.197

Gnomad OTH exome

AF:

0.134

GnomAD4 exome

AF:

0.272

AC:

358538

AN:

1317686

Hom.:

50215

AF XY:

0.269

AC XY:

177123

AN XY:

659148

show subpopulations

Gnomad4 AFR exome

AF:

0.124

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.242

Gnomad4 EAS exome

AF:

0.156

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.239

Gnomad4 NFE exome

AF:

0.299

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.234

AC:

35591

AN:

152162

Hom.:

4628

Cov.:

AF XY:

0.230

AC XY:

17135

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.263

Gnomad4 EAS

AF:

0.169

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.223

Hom.:

843

Asia WGS

AF:

0.161

AC:

557

AN:

3470

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

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