rs7967521

Variant names:

• chr12-124832224-T-C
• rs7967521
• NM_005505.5:c.127-14517A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-124832224-T-C
• chr12-124832224-T-G

Variant summary

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

The NM_005505.5(SCARB1):​c.127-14517A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,078 control chromosomes in the GnomAD database, including 19,586 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 0.50 (19586 hom., cov: 33)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 15 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 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.127-14517A>G		intron	N/A	NP_005496.4
	SCARB1	NM_001367981.1		c.127-14517A>G		intron	N/A	NP_001354910.1	Q8WTV0-1
	SCARB1	NM_001367982.1		c.3+7020A>G		intron	N/A	NP_001354911.1	B3KW46

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.127-14517A>G		intron	N/A	ENSP00000261693.6	Q8WTV0-2
	SCARB1	ENST00000546215.5	TSL:1	c.127-14517A>G		intron	N/A	ENSP00000442862.1	B7ZKQ9
	SCARB1	ENST00000535005.5	TSL:1	n.442-14517A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76085 AN: 151960 Hom.: 19568 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.501 AC: 76145 AN: 152078 Hom.: 19586 Cov.: 33 AF XY: 0.499 AC XY: 37123 AN XY: 74326

African (AFR) AF: 0.398 AC: 16507 AN: 41470

American (AMR) AF: 0.446 AC: 6819 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2307 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1700 AN: 5172

South Asian (SAS) AF: 0.524 AC: 2526 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5773 AN: 10570

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38517 AN: 67980

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.542 Hom.: 93014

Bravo AF: 0.487

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.89
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: rs7967521; hg19: chr12-125316770;