rs838905

chr12-124806460-A-Gchr12-124806460-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.1009+1301T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,130 control chromosomes in the GnomAD database, including 4,640 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 0.18 (4640 hom., cov: 32)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARB1	NM_005505.5	c.1009+1301T>C		intron_variant		ENST00000261693.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000261693.11	c.1009+1301T>C		intron_variant		1	NM_005505.5	P3
	ENST00000657226.1	n.1126-1150A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27286 AN: 152012 Hom.: 4608 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.180 AC: 27371 AN: 152130 Hom.: 4640 Cov.: 32 AF XY: 0.182 AC XY: 13538 AN XY: 74396

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0508

Gnomad4 NFE AF: 0.0411

Gnomad4 OTH AF: 0.157

Alfa AF: 0.0835 Hom.: 2114

Bravo AF: 0.210

Asia WGS AF: 0.279 AC: 968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.41

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: rs838905; hg19: chr12-125291006;