rs11057852

Variant names:

• chr12-124844280-C-T
• rs11057852
• NM_005505.5:c.126+19315G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005505.5(SCARB1):​c.126+19315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 152,162 control chromosomes in the GnomAD database, including 310 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 0.059 (310 hom., cov: 32)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.126+19315G>A		intron_variant	Intron 1 of 12	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.126+19315G>A		intron_variant	Intron 1 of 12	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8906 AN: 152044 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0587 AC: 8927 AN: 152162 Hom.: 310 Cov.: 32 AF XY: 0.0567 AC XY: 4214 AN XY: 74380

African (AFR) AF: 0.0917 AC: 3808 AN: 41512

American (AMR) AF: 0.0452 AC: 690 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.0782 AC: 405 AN: 5176

South Asian (SAS) AF: 0.0455 AC: 219 AN: 4814

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3095 AN: 67996

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0527 Hom.: 219

Bravo AF: 0.0624

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.66
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11057852; hg19: chr12-125328826;