rs11045892

Variant names:

• chr12-21239860-A-G
• rs11045892
• XR_007063239.1:n.87-5561T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063239.1(LOC124902895):​n.87-5561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,232 control chromosomes in the GnomAD database, including 1,661 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 0.13 (1661 hom., cov: 33)
• Consequence: LOC124902895 XR_007063239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

LOC124902895 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902895	XR_007063239.1	n.87-5561T>C		intron_variant	Intron 1 of 1
SLCO1B1	NM_006446.5	c.*671A>G		downstream_gene_variant		ENST00000256958.3	NP_006437.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1B1	ENST00000256958.3	c.*671A>G		downstream_gene_variant		1	NM_006446.5	ENSP00000256958.2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20314 AN: 152114 Hom.: 1664 Cov.: 33

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.133 AC: 20313 AN: 152232 Hom.: 1661 Cov.: 33 AF XY: 0.128 AC XY: 9515 AN XY: 74444

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.135

Alfa AF: 0.172 Hom.: 2297

Bravo AF: 0.133

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11045892; hg19: chr12-21392794;