12-20958862-C-T

Variant names:

• chr12-20958862-C-T
• rs2217694
• ENST00000540229.1:c.1865+57395C>T

Variant summary

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

The ENST00000540229.1(SLCO1B3-SLCO1B7):​c.1865+57395C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,034 control chromosomes in the GnomAD database, including 50,853 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 0.78 (50853 hom., cov: 31)
• Consequence: SLCO1B3-SLCO1B7 ENST00000540229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1	c.1865+57395C>T		intron_variant	Intron 13 of 15		NP_001358026.1
LOC124902894	XM_047429949.1	c.-57-56777C>T		intron_variant	Intron 1 of 9		XP_047285905.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1B3-SLCO1B7	ENST00000540229.1	c.1865+57395C>T		intron_variant	Intron 13 of 15	2		ENSP00000441269.1
SLCO1B3-SLCO1B7	ENST00000381541.7	c.360-62599C>T		intron_variant	Intron 3 of 13	2		ENSP00000370952.3

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118175 AN: 151916 Hom.: 50839 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.778 AC: 118224 AN: 152034 Hom.: 50853 Cov.: 31 AF XY: 0.782 AC XY: 58156 AN XY: 74356

African (AFR) AF: 0.371 AC: 15363 AN: 41400

American (AMR) AF: 0.896 AC: 13682 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3244 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4741 AN: 5164

South Asian (SAS) AF: 0.952 AC: 4600 AN: 4830

European-Finnish (FIN) AF: 0.903 AC: 9560 AN: 10592

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.944 AC: 64155 AN: 67992

Other (OTH) AF: 0.821 AC: 1733 AN: 2110

Alfa AF: 0.802 Hom.: 7084

Bravo AF: 0.760

Asia WGS AF: 0.887 AC: 3082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.58
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2217694; hg19: chr12-21111796;