rs838892

Variant names:

• chr12-124784777-A-C
• rs838892
• NM_005505.5:c.1401+1580T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-124784777-A-C
• chr12-124784777-A-G
• chr12-124784777-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.1401+1580T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,320 control chromosomes in the GnomAD database, including 31,749 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 (31706 hom., cov: 33)
  • Exomes 𝑓: 0.66 (43 hom.)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.1401+1580T>G		intron_variant	Intron 11 of 12	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.1401+1580T>G		intron_variant	Intron 11 of 12	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97334 AN: 152000 Hom.: 31698 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.663 AC: 134 AN: 202 Hom.: 43 Cov.: 0 AF XY: 0.667 AC XY: 100 AN XY: 150

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.375 AC: 3 AN: 8

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.674 AC: 120 AN: 178

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.640 AC: 97370 AN: 152118 Hom.: 31706 Cov.: 33 AF XY: 0.638 AC XY: 47410 AN XY: 74360

African (AFR) AF: 0.614 AC: 25465 AN: 41496

American (AMR) AF: 0.532 AC: 8131 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1898 AN: 5154

South Asian (SAS) AF: 0.762 AC: 3678 AN: 4828

European-Finnish (FIN) AF: 0.640 AC: 6780 AN: 10590

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46704 AN: 67966

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.673 Hom.: 148539

Bravo AF: 0.628

Asia WGS AF: 0.572 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		0.22
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: rs838892; hg19: chr12-125269323;