12-20921188-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001371097.1(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 NM_001371097.1 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.50

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1	c.1865+19721C>T		intron_variant	Intron 13 of 15		NP_001358026.1
LOC124902894	XM_047429949.1	c.-58+19721C>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+19721C>T		intron_variant	Intron 13 of 15	2		ENSP00000441269.1
SLCO1B3-SLCO1B7	ENST00000381541.7	c.359+62617C>T		intron_variant	Intron 3 of 13	2		ENSP00000370952.3

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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.489

Alfa AF: 0.599 Hom.: 32954

Bravo AF: 0.461

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Gilbert syndrome Benign:1

May 01, 2019

Difficult and Complicated Liver Diseases and Artificial Liver Center, Beijing You An Hospital, Capital Medical University

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

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