rs701106

chr12-124781090-A-Gchr12-124781090-A-T

Variant summary

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

The NM_005505.5(SCARB1):c.*1593T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,124 control chromosomes in the GnomAD database, including 49,663 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 0.81 (49663 hom., cov: 33)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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 (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARB1	NM_005505.5	c.*1593T>C		intron_variant		ENST00000261693.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000261693.11	c.*1593T>C		intron_variant		1	NM_005505.5	P3

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122647 AN: 152006 Hom.: 49635 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.807 AC: 122729 AN: 152124 Hom.: 49663 Cov.: 33 AF XY: 0.804 AC XY: 59802 AN XY: 74356

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.821

Alfa AF: 0.833 Hom.: 67888

Bravo AF: 0.813

Asia WGS AF: 0.860 AC: 2991 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	0.71
Dann	Benign	0.45

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: rs701106; hg19: chr12-125265636;