chr12-124814823-A-G

Variant names:

• chr12-124814823-A-G
• rs2278986
• NM_005505.5:c.426+150T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005505.5(SCARB1):​c.426+150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 943,434 control chromosomes in the GnomAD database, including 45,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6327 hom., cov: 32)
  • Exomes 𝑓: 0.31 (39311 hom.)
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.187
• Publications: 16 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 12-124814823-A-G is Benign according to our data. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in CliVar as Benign. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.426+150T>C		intron_variant	Intron 3 of 12	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.426+150T>C		intron_variant	Intron 3 of 12	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42746 AN: 152054 Hom.: 6312 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.308 AC: 243487 AN: 791262 Hom.: 39311 AF XY: 0.316 AC XY: 129676 AN XY: 410440

African (AFR) AF: 0.218 AC: 4401 AN: 20160

American (AMR) AF: 0.244 AC: 8522 AN: 34868

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 9498 AN: 21060

East Asian (EAS) AF: 0.182 AC: 6020 AN: 33044

South Asian (SAS) AF: 0.440 AC: 29254 AN: 66438

European-Finnish (FIN) AF: 0.242 AC: 8698 AN: 35880

Middle Eastern (MID) AF: 0.353 AC: 1086 AN: 3078

European-Non Finnish (NFE) AF: 0.305 AC: 164083 AN: 538572

Other (OTH) AF: 0.312 AC: 11925 AN: 38162

GnomAD4 genome AF: 0.281 AC: 42796 AN: 152172 Hom.: 6327 Cov.: 32 AF XY: 0.282 AC XY: 21014 AN XY: 74388

African (AFR) AF: 0.216 AC: 8984 AN: 41554

American (AMR) AF: 0.275 AC: 4209 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1152 AN: 5152

South Asian (SAS) AF: 0.441 AC: 2128 AN: 4826

European-Finnish (FIN) AF: 0.238 AC: 2524 AN: 10598

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21071 AN: 67970

Other (OTH) AF: 0.311 AC: 658 AN: 2114

Alfa AF: 0.301 Hom.: 892

Bravo AF: 0.275

Asia WGS AF: 0.375 AC: 1301 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 17, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.57
PhyloP100		-0.19
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: rs2278986; hg19: chr12-125299369; COSMIC: COSV55549668; COSMIC: COSV55549668;