Variant rs838897 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005505.5(SCARB1):c.1255-41C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 1,610,992 control chromosomes in the GnomAD database, including 14,095 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 3770 hom., cov: 33)

Exomes 𝑓: 0.073 ( 10325 hom. )

Consequence

SCARB1
NM_005505.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00600

Variant links:

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]

SCARB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 12-124786544-G-C is Benign according to our data. Variant chr12-124786544-G-C is described in ClinVar as [Benign]. Clinvar id is 1232985.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-124786544-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARB1	NM_005505.5 linkuse as main transcript	c.1255-41C>G		intron_variant		ENST00000261693.11	NP_005496.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11 linkuse as main transcript	c.1255-41C>G		intron_variant		1	NM_005505.5	ENSP00000261693	P3	Q8WTV0-2

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25122

AN:

152122

Hom.:

3740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.0793

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0586

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0447

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.138

AC:

33822

AN:

245882

Hom.:

4715

AF XY:

0.122

AC XY:

16224

AN XY:

133304

show subpopulations

Gnomad AFR exome

AF:

0.373

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.0747

Gnomad EAS exome

AF:

0.436

Gnomad SAS exome

AF:

0.0826

Gnomad FIN exome

AF:

0.0588

Gnomad NFE exome

AF:

0.0450

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.0732

AC:

106831

AN:

1458752

Hom.:

10325

Cov.:

AF XY:

0.0719

AC XY:

52177

AN XY:

725670

show subpopulations

Gnomad4 AFR exome

AF:

0.372

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.0759

Gnomad4 EAS exome

AF:

0.446

Gnomad4 SAS exome

AF:

0.0839

Gnomad4 FIN exome

AF:

0.0565

Gnomad4 NFE exome

AF:

0.0404

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.166

AC:

25207

AN:

152240

Hom.:

3770

Cov.:

AF XY:

0.167

AC XY:

12408

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.364

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.0793

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.0991

Gnomad4 FIN

AF:

0.0586

Gnomad4 NFE

AF:

0.0446

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.102

Hom.:

307

Bravo

AF:

0.190

Asia WGS

AF:

0.264

AC:

919

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 01, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.0

DANN

Benign

0.61

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over