12-20921188-C-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:):

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/exons	MANE	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1	c.1865+19721C>T		intron_variant
LOC124902894	XM_047429949.1	c.-58+19721C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Benign, no assertion criteria provided

case-control

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

May 01, 2019

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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;