rs7306660

Variant names:

• chr12-124842838-G-A
• rs7306660
• NM_005505.5:c.126+20757C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-124842838-G-A
• chr12-124842838-G-C

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+20757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,102 control chromosomes in the GnomAD database, including 10,920 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 0.38 (10920 hom., cov: 33)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 10 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	NM_005505.5	MANE Select	c.126+20757C>T		intron	N/A	NP_005496.4
	SCARB1	NM_001367981.1		c.126+20757C>T		intron	N/A	NP_001354910.1
	SCARB1	NM_001367983.1		c.126+20757C>T		intron	N/A	NP_001354912.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.126+20757C>T		intron	N/A	ENSP00000261693.6
	SCARB1	ENST00000546215.5	TSL:1	c.126+20757C>T		intron	N/A	ENSP00000442862.1
	SCARB1	ENST00000535005.5	TSL:1	n.441+24151C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57046 AN: 151984 Hom.: 10889 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.376 AC: 57121 AN: 152102 Hom.: 10920 Cov.: 33 AF XY: 0.375 AC XY: 27886 AN XY: 74358

African (AFR) AF: 0.399 AC: 16543 AN: 41470

American (AMR) AF: 0.456 AC: 6967 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2111 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4824

European-Finnish (FIN) AF: 0.300 AC: 3180 AN: 10588

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23955 AN: 67982

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.369 Hom.: 35908

Bravo AF: 0.391

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		-0.24
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: rs7306660; hg19: chr12-125327384;