ENST00000540229.1:c.1865+19721C>T

Variant names:

• chr12-20921188-C-T
• rs2117032
• ENST00000540229.1:c.1865+19721C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000540229.1(SLCO1B3-SLCO1B7):​c.1865+19721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,146 control chromosomes in the GnomAD database, including 20,725 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.48 (20725 hom., cov: 32)
• Consequence: SLCO1B3-SLCO1B7 ENST00000540229.1 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.50
• Publications: 30 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 12-20921188-C-T is Benign according to our data. Variant chr12-20921188-C-T is described in ClinVar as Benign. ClinVar VariationId is 810735.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540229.1. 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
	SLCO1B3-SLCO1B7	NM_001371097.1		c.1865+19721C>T		intron	N/A	NP_001358026.1	A0A0A6YYJ9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO1B3-SLCO1B7	ENST00000540229.1	TSL:2	c.1865+19721C>T		intron	N/A	ENSP00000441269.1
	SLCO1B3-SLCO1B7	ENST00000381541.7	TSL:2	c.359+62617C>T		intron	N/A	ENSP00000370952.3	F5H094-1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72373 AN: 151028 Hom.: 20717 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.479 AC: 72387 AN: 151146 Hom.: 20725 Cov.: 32 AF XY: 0.483 AC XY: 35712 AN XY: 73878

African (AFR) AF: 0.147 AC: 6106 AN: 41410

American (AMR) AF: 0.533 AC: 8067 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1809 AN: 3446

East Asian (EAS) AF: 0.555 AC: 2864 AN: 5160

South Asian (SAS) AF: 0.742 AC: 3572 AN: 4816

European-Finnish (FIN) AF: 0.579 AC: 6086 AN: 10512

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42166 AN: 67354

Other (OTH) AF: 0.489 AC: 1027 AN: 2102

Alfa AF: 0.582 Hom.: 80872

Bravo AF: 0.461

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	Gilbert syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.30
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: rs2117032; hg19: chr12-21074122;