rs838881

Positions:

• chr12-124777251-G-A
• chr12-124777251-G-C
• chr12-124777251-G-T

Variant summary

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

The NM_005505.5(SCARB1):​c.*1336C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,838 control chromosomes in the GnomAD database, including 29,347 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 0.60 (29346 hom., cov: 31)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: SCARB1 NM_005505.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

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]

SCARB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.*1336C>T		3_prime_UTR_variant	13/13	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.*1336C>T		3_prime_UTR_variant	13/13	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91518 AN: 151714 Hom.: 29337 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.653

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.603 AC: 91563 AN: 151832 Hom.: 29346 Cov.: 31 AF XY: 0.602 AC XY: 44677 AN XY: 74208

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.650

Alfa AF: 0.573 Hom.: 2371

Bravo AF: 0.608

Asia WGS AF: 0.702 AC: 2441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs838881; hg19: chr12-125261797;