rs7977729

chr12-124781886-T-C

Variant summary

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

The NM_005505.5(SCARB1):c.*797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,036 control chromosomes in the GnomAD database, including 4,534 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 0.22 (4534 hom., cov: 32)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARB1	NM_005505.5	c.*797A>G		intron_variant		ENST00000261693.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000261693.11	c.*797A>G		intron_variant		1	NM_005505.5	P3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33647 AN: 151918 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.221 AC: 33648 AN: 152036 Hom.: 4534 Cov.: 32 AF XY: 0.222 AC XY: 16466 AN XY: 74330

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.257

Alfa AF: 0.260 Hom.: 1494

Bravo AF: 0.214

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.0
Dann	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7977729; hg19: chr12-125266432;