12-21141292-AATTT-A

Position:

• chr12-21141292-AATTT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006446.5(SLCO1B1):​c.-61-217_-61-214delATTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 151,800 control chromosomes in the GnomAD database, including 274 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.050 (274 hom., cov: 31)
• Consequence: SLCO1B1 NM_006446.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.59

Genes affected

SLCO1B1 (HGNC:10959): (solute carrier organic anion transporter family member 1B1) 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 numerous endogenous compounds including bilirubin, 17-beta-glucuronosyl estradiol and leukotriene C4. This protein is also involved in the removal of drug compounds such as statins, bromosulfophthalein and rifampin from the blood into the hepatocytes. Polymorphisms in the gene encoding this protein are associated with impaired transporter function. [provided by RefSeq, Mar 2009]

ENSG00000257062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-21141292-AATTT-A is Benign according to our data. Variant chr12-21141292-AATTT-A is described in ClinVar as [Benign]. Clinvar id is 1225618.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO1B1	NM_006446.5	c.-61-217_-61-214delATTT		intron_variant		ENST00000256958.3	NP_006437.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO1B1	ENST00000256958.3	c.-61-217_-61-214delATTT		intron_variant		1	NM_006446.5	ENSP00000256958.2

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7569 AN: 151682 Hom.: 274 Cov.: 31

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0662

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0499 AC: 7571 AN: 151800 Hom.: 274 Cov.: 31 AF XY: 0.0517 AC XY: 3836 AN XY: 74194

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0446

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.0670

Alfa AF: 0.0288 Hom.: 22

Asia WGS AF: 0.0680 AC: 236 AN: 3464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs4149092; hg19: chr12-21294226;