Variant rs5892 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_005505.5(SCARB1):c.903C>T(p.Phe301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,614,072 control chromosomes in the GnomAD database, including 414 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.026 ( 121 hom., cov: 32)

Exomes 𝑓: 0.011 ( 293 hom. )

Consequence

SCARB1
NM_005505.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0290

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 12-124807867-G-A is Benign according to our data. Variant chr12-124807867-G-A is described in ClinVar as [Benign]. Clinvar id is 1224092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-124807867-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.029 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARB1	NM_005505.5 linkuse as main transcript	c.903C>T	p.Phe301=	synonymous_variant	7/13	ENST00000261693.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000261693.11 linkuse as main transcript	c.903C>T	p.Phe301=	synonymous_variant	7/13	1	NM_005505.5	P3	Q8WTV0-2
	ENST00000657226.1 linkuse as main transcript	n.1383G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes

AF:

0.0258

AC:

3932

AN:

152126

Hom.:

115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00851

Gnomad ASJ

AF:

0.0161

Gnomad EAS

AF:

0.0399

Gnomad SAS

AF:

0.0493

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00575

Gnomad OTH

AF:

0.0216

GnomAD3 exomes

AF:

0.0177

AC:

4450

AN:

251478

Hom.:

AF XY:

0.0180

AC XY:

2452

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.0675

Gnomad AMR exome

AF:

0.00610

Gnomad ASJ exome

AF:

0.0135

Gnomad EAS exome

AF:

0.0421

Gnomad SAS exome

AF:

0.0446

Gnomad FIN exome

AF:

0.00106

Gnomad NFE exome

AF:

0.00667

Gnomad OTH exome

AF:

0.0138

GnomAD4 exome

AF:

0.0108

AC:

15782

AN:

1461828

Hom.:

293

Cov.:

AF XY:

0.0116

AC XY:

8423

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.0780

Gnomad4 AMR exome

AF:

0.00713

Gnomad4 ASJ exome

AF:

0.0135

Gnomad4 EAS exome

AF:

0.0284

Gnomad4 SAS exome

AF:

0.0424

Gnomad4 FIN exome

AF:

0.00110

Gnomad4 NFE exome

AF:

0.00577

Gnomad4 OTH exome

AF:

0.0186

GnomAD4 genome

AF:

0.0261

AC:

3967

AN:

152244

Hom.:

121

Cov.:

AF XY:

0.0264

AC XY:

1963

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0692

Gnomad4 AMR

AF:

0.00849

Gnomad4 ASJ

AF:

0.0161

Gnomad4 EAS

AF:

0.0400

Gnomad4 SAS

AF:

0.0487

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00575

Gnomad4 OTH

AF:

0.0237

Alfa

AF:

0.0112

Hom.:

Bravo

AF:

0.0281

Asia WGS

AF:

0.0610

AC:

210

AN:

3478

EpiCase

AF:

0.00562

EpiControl

AF:

0.00788

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	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 04, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.87

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