12-124788217-A-T

Variant names:

• chr12-124788217-A-T
• rs9919713
• NM_005505.5:c.1203-760T>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.1203-760T>A 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 152,052 control chromosomes in the GnomAD database, including 4,491 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 (4491 hom., cov: 32)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 7 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]

ENSG00000287242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.1203-760T>A		intron_variant	Intron 9 of 12	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.1203-760T>A		intron_variant	Intron 9 of 12	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27350 AN: 151934 Hom.: 4465 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0471

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.180 AC: 27434 AN: 152052 Hom.: 4491 Cov.: 32 AF XY: 0.181 AC XY: 13437 AN XY: 74330

African (AFR) AF: 0.412 AC: 17066 AN: 41424

American (AMR) AF: 0.210 AC: 3199 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2173 AN: 5158

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.0587 AC: 623 AN: 10614

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0471 AC: 3202 AN: 67992

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.120 Hom.: 300

Bravo AF: 0.205

Asia WGS AF: 0.261 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.49
PhyloP100		-2.0
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: rs9919713; hg19: chr12-125272763;