Genetic Variant SCARB1:n.293-89G>A (chr12-124867226-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000535005.5(SCARB1):n.293-89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,172 control chromosomes in the GnomAD database, including 6,443 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 0.27 ( 6442 hom., cov: 33)

Exomes 𝑓: 0.38 ( 1 hom. )

Consequence

SCARB1
ENST00000535005.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.02

Publications

8 publications found

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:

LOC105370050 (HGNC:):

LOC105370050 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370050	XR_945488.3 link	n.1622+550C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000535005.5 link	n.293-89G>A		intron_variant	Intron 1 of 12	1
SCARB1	ENST00000541661.5 link	n.167+15276G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40909

AN:

152038

Hom.:

6440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.269

AC:

40917

AN:

152156

Hom.:

6442

Cov.:

AF XY:

0.271

AC XY:

20123

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0999

AC:

4150

AN:

41534

American (AMR)

AF:

0.324

AC:

4947

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.295

AC:

1023

AN:

3468

East Asian (EAS)

AF:

0.240

AC:

1245

AN:

5180

South Asian (SAS)

AF:

0.273

AC:

1315

AN:

4820

European-Finnish (FIN)

AF:

0.343

AC:

3627

AN:

10566

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23662

AN:

67980

Other (OTH)

AF:

0.306

AC:

646

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1475

2950

4424

5899

7374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.282

Hom.:

5915

Bravo

AF:

0.257

Asia WGS

AF:

0.284

AC:

986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.029

(source)

DANN

Benign

0.44

PhyloP100

-4.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over