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:54403): (SLCO1B3-SLCO1B7 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring SLCO1B3 (solute carrier organic anion transporter family member 1B3) and SLCO1B7 (solute carrier organic anion transporter family member 1B7 (putative)) genes on chromosome 12. The readthrough transcript encodes a protein that shares sequence identity with both the upstream and downstream genes. [provided by RefSeq, Jun 2019]

LOC124902894 (HGNC:):

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
SLCO1B3-SLCO1B7	ENST00000540229.1	c.1866-53930G>A		intron_variant		2		ENSP00000441269.1
SLCO1B3-SLCO1B7	ENST00000381541.7	c.360-8072G>A		intron_variant		2		ENSP00000370952.3
SLCO1B7	ENST00000648739.1	n.85-2250G>A		intron_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;