Genetic Variant SCARB1:c.1401+1428A>G (chr12-124784929-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005505.5(SCARB1):c.1401+1428A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,320 control chromosomes in the GnomAD database, including 31,830 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 0.64 ( 31779 hom., cov: 34)

Exomes 𝑓: 0.74 ( 51 hom. )

Consequence

SCARB1
NM_005505.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.840

Publications

10 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:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARB1	NM_005505.5 link	c.1401+1428A>G		intron_variant	Intron 11 of 12	ENST00000261693.11	NP_005496.4	Q8WTV0-2A0A024RBS4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARB1	ENST00000261693.11 link	c.1401+1428A>G		intron_variant	Intron 11 of 12	1	NM_005505.5	ENSP00000261693.6		Q8WTV0-2

Frequencies

GnomAD3 genomes

AF:

0.641

AC:

97452

AN:

152008

Hom.:

31770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.533

Gnomad ASJ

AF:

0.716

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.762

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.691

Gnomad NFE

AF:

0.688

Gnomad OTH

AF:

0.632

GnomAD4 exome

AF:

0.742

AC:

144

AN:

194

Hom.:

Cov.:

AF XY:

0.754

AC XY:

AN XY:

130

show subpopulations

African (AFR)

AF:

0.833

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.656

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.742

AC:

AN:

128

Other (OTH)

AF:

0.773

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

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:

0.641

AC:

97489

AN:

152126

Hom.:

31779

Cov.:

AF XY:

0.638

AC XY:

47434

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.615

AC:

25509

AN:

41510

American (AMR)

AF:

0.532

AC:

8138

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.716

AC:

2483

AN:

3466

East Asian (EAS)

AF:

0.367

AC:

1900

AN:

5174

South Asian (SAS)

AF:

0.763

AC:

3687

AN:

4830

European-Finnish (FIN)

AF:

0.640

AC:

6782

AN:

10592

Middle Eastern (MID)

AF:

0.705

AC:

206

AN:

292

European-Non Finnish (NFE)

AF:

0.688

AC:

46746

AN:

67960

Other (OTH)

AF:

0.630

AC:

1328

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1801

3603

5404

7206

9007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<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:

0.684

Hom.:

18296

Bravo

AF:

0.629

Asia WGS

AF:

0.575

AC:

2001

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.8

(source)

DANN

Benign

0.55

PhyloP100

-0.84

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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