12-20958862-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371097.1(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 NM_001371097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

SLCO1B3-SLCO1B7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1	c.1865+57395C>T		intron_variant
LOC124902894	XM_047429949.1	c.-57-56777C>T		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.821

Alfa AF: 0.817 Hom.: 7015

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

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: rs2217694; hg19: chr12-21111796;