rs3782287

Variant names:

• chr12-124804719-G-A
• rs3782287
• NM_005505.5:c.1009+3042C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-124804719-G-A
• chr12-124804719-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367981.1(SCARB1):​c.1009+3042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,086 control chromosomes in the GnomAD database, including 13,139 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 0.40 (13139 hom., cov: 33)
• Consequence: SCARB1 NM_001367981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 26 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367981.1. 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.1009+3042C>T		intron	N/A	NP_005496.4
	SCARB1	NM_001367981.1		c.1009+3042C>T		intron	N/A	NP_001354910.1
	SCARB1	NM_001367982.1		c.886+3042C>T		intron	N/A	NP_001354911.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.1009+3042C>T		intron	N/A	ENSP00000261693.6
	SCARB1	ENST00000546215.5	TSL:1	c.1009+3042C>T		intron	N/A	ENSP00000442862.1
	SCARB1	ENST00000535005.5	TSL:1	n.1324+3042C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61436 AN: 151966 Hom.: 13136 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.404 AC: 61453 AN: 152086 Hom.: 13139 Cov.: 33 AF XY: 0.407 AC XY: 30226 AN XY: 74348

African (AFR) AF: 0.281 AC: 11675 AN: 41522

American (AMR) AF: 0.363 AC: 5554 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3464

East Asian (EAS) AF: 0.260 AC: 1342 AN: 5164

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5878 AN: 10566

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32234 AN: 67944

Other (OTH) AF: 0.420 AC: 887 AN: 2114

Alfa AF: 0.447 Hom.: 67111

Bravo AF: 0.383

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs3782287; hg19: chr12-125289265;