rs4765181

Variant names:

• chr12-124854682-A-C
• rs4765181
• NM_005505.5:c.126+8913T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-124854682-A-C
• chr12-124854682-A-G
• chr12-124854682-A-T

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+8913T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,922 control chromosomes in the GnomAD database, including 31,271 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 0.64 (31271 hom., cov: 31)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005505.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	NM_005505.5	MANE Select	c.126+8913T>G		intron	N/A	NP_005496.4
	SCARB1	NM_001367981.1		c.126+8913T>G		intron	N/A	NP_001354910.1	Q8WTV0-1
	SCARB1	NM_001367983.1		c.126+8913T>G		intron	N/A	NP_001354912.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.126+8913T>G		intron	N/A	ENSP00000261693.6	Q8WTV0-2
	SCARB1	ENST00000546215.5	TSL:1	c.126+8913T>G		intron	N/A	ENSP00000442862.1	B7ZKQ9
	SCARB1	ENST00000535005.5	TSL:1	n.441+12307T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97008 AN: 151804 Hom.: 31210 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.639 AC: 97133 AN: 151922 Hom.: 31271 Cov.: 31 AF XY: 0.640 AC XY: 47557 AN XY: 74252

African (AFR) AF: 0.697 AC: 28858 AN: 41422

American (AMR) AF: 0.655 AC: 9999 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3585 AN: 5146

South Asian (SAS) AF: 0.582 AC: 2800 AN: 4812

European-Finnish (FIN) AF: 0.616 AC: 6509 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41154 AN: 67934

Other (OTH) AF: 0.646 AC: 1361 AN: 2108

Alfa AF: 0.614 Hom.: 49854

Bravo AF: 0.644

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.20
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4765181; hg19: chr12-125339228;