12-124778698-G-C

Variant names:

• chr12-124778698-G-C
• rs747155
• NM_005505.5:c.*1-112C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_005505.5(SCARB1):​c.*1-112C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCARB1 NM_005505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5	c.*1-112C>G		intron_variant	Intron 12 of 12	ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11	c.*1-112C>G		intron_variant	Intron 12 of 12	1	NM_005505.5	ENSP00000261693.6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 39132 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 917694 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 441186

African (AFR) AF: 0.00 AC: 0 AN: 19390

American (AMR) AF: 0.00 AC: 0 AN: 8264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13636

East Asian (EAS) AF: 0.00 AC: 0 AN: 25644

South Asian (SAS) AF: 0.00 AC: 0 AN: 21552

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29654

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2670

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 758422

Other (OTH) AF: 0.00 AC: 0 AN: 38462

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 39132 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 18794

African (AFR) AF: 0.00 AC: 0 AN: 13974

American (AMR) AF: 0.00 AC: 0 AN: 2378

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 878

East Asian (EAS) AF: 0.00 AC: 0 AN: 1032

South Asian (SAS) AF: 0.00 AC: 0 AN: 1134

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1820

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 48

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 17190

Other (OTH) AF: 0.00 AC: 0 AN: 490

Alfa AF: 0.00 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.44
DANN	Benign	0.42
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs747155; hg19: chr12-125263244;