rs10744182

chr12-124833036-C-T

Variant summary

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

The NM_005505.5(SCARB1):c.127-15329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,598 control chromosomes in the GnomAD database, including 20,217 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 0.50 (20217 hom., cov: 29)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

SCARB1 (HGNC:1664): (scavenger receptor class B member 1) The protein encoded by this gene is a plasma membrane receptor for high density lipoprotein cholesterol (HDL). The encoded protein mediates cholesterol transfer to and from HDL. In addition, this protein is a receptor for hepatitis C virus glycoprotein E2 and facilitates cell entry by the virus, SARS-CoV2. [provided by RefSeq, Oct 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARB1	NM_005505.5	c.127-15329G>A		intron_variant		ENST00000261693.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000261693.11	c.127-15329G>A		intron_variant		1	NM_005505.5	P3

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75065 AN: 151480 Hom.: 20219 Cov.: 29

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.495 AC: 75063 AN: 151598 Hom.: 20217 Cov.: 29 AF XY: 0.497 AC XY: 36830 AN XY: 74066

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.568

Alfa AF: 0.570 Hom.: 19103

Bravo AF: 0.480

Asia WGS AF: 0.489 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.26
Dann	Benign	0.38

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: rs10744182; hg19: chr12-125317582;