rs2417873

Positions:

• chr12-21013389-G-A

Variant summary

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

The NM_001371097.1(SLCO1B3-SLCO1B7):​c.1866-53930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,128 control chromosomes in the GnomAD database, including 15,681 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 (15681 hom., cov: 32)
• Consequence: SLCO1B3-SLCO1B7 NM_001371097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

SLCO1B3-SLCO1B7 (HGNC:):

SLCO1B7 (HGNC:32934): (solute carrier organic anion transporter family member 1B7 (putative)) Predicted to enable bile acid transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in bile acid and bile salt transport and sodium-independent organic anion transport. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1	c.1866-53930G>A		intron_variant			NP_001358026.1
LOC124902894	XM_047429949.1	c.-57-2250G>A		intron_variant			XP_047285905.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO1B7	ENST00000648739.1	n.85-2250G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59409 AN: 152010 Hom.: 15639 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.391 AC: 59501 AN: 152128 Hom.: 15681 Cov.: 32 AF XY: 0.379 AC XY: 28166 AN XY: 74360

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.375

Alfa AF: 0.285 Hom.: 14007

Bravo AF: 0.417

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.30

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: rs2417873; hg19: chr12-21166323;