12-21240084-T-G

Variant names:

• chr12-21240084-T-G
• rs12372157
• ENST00000870182.1:c.*895T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000870182.1(SLCO1B1):​c.*895T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,010 control chromosomes in the GnomAD database, including 12,563 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (12563 hom., cov: 32)
• Consequence: SLCO1B1 ENST00000870182.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 7 publications found

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]

SLCO1B1 Gene-Disease associations (from GenCC):

• Rotor syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

LOC124902895 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000870182.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO1B1	ENST00000870182.1		c.*895T>G		3_prime_UTR	Exon 16 of 16	ENSP00000540241.1
	SLCO1B1	ENST00000870178.1		c.*895T>G		3_prime_UTR	Exon 15 of 15	ENSP00000540237.1
	SLCO1B1	ENST00000870179.1		c.*895T>G		3_prime_UTR	Exon 14 of 14	ENSP00000540238.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59899 AN: 151892 Hom.: 12555 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.394 AC: 59938 AN: 152010 Hom.: 12563 Cov.: 32 AF XY: 0.401 AC XY: 29788 AN XY: 74290

African (AFR) AF: 0.287 AC: 11906 AN: 41474

American (AMR) AF: 0.391 AC: 5969 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.734 AC: 3787 AN: 5158

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4822

European-Finnish (FIN) AF: 0.485 AC: 5117 AN: 10554

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28067 AN: 67946

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.407 Hom.: 21333

Bravo AF: 0.387

Asia WGS AF: 0.572 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.46
PhyloP100		-0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12372157; hg19: chr12-21393018;