dbSNP rs2278986: SCARB1:c.426+150T>C (chr12-124814823-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005505.5(SCARB1):c.426+150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 943,434 control chromosomes in the GnomAD database, including 45,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6327 hom., cov: 32)

Exomes 𝑓: 0.31 ( 39311 hom. )

Consequence

SCARB1
NM_005505.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.187

Publications

16 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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_005505.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 12-124814823-A-G is Benign according to our data. Variant chr12-124814823-A-G is described in ClinVar as Benign. ClinVar VariationId is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005505.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SCARB1	NM_005505.5	MANE Select	c.426+150T>C	intron	N/A	NP_005496.4
SCARB1	NM_001367981.1		c.426+150T>C	intron	N/A	NP_001354910.1	Q8WTV0-1
SCARB1	NM_001367982.1		c.303+150T>C	intron	N/A	NP_001354911.1	B3KW46

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.426+150T>C	intron	N/A	ENSP00000261693.6	Q8WTV0-2
SCARB1	ENST00000546215.5	TSL:1	c.426+150T>C	intron	N/A	ENSP00000442862.1	B7ZKQ9
SCARB1	ENST00000535005.5	TSL:1	n.741+150T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42746

AN:

152054

Hom.:

6312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.363

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.306

GnomAD4 exome

AF:

0.308

AC:

243487

AN:

791262

Hom.:

39311

AF XY:

0.316

AC XY:

129676

AN XY:

410440

show subpopulations

African (AFR)

AF:

0.218

AC:

4401

AN:

20160

American (AMR)

AF:

0.244

AC:

8522

AN:

34868

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

9498

AN:

21060

East Asian (EAS)

AF:

0.182

AC:

6020

AN:

33044

South Asian (SAS)

AF:

0.440

AC:

29254

AN:

66438

European-Finnish (FIN)

AF:

0.242

AC:

8698

AN:

35880

Middle Eastern (MID)

AF:

0.353

AC:

1086

AN:

3078

European-Non Finnish (NFE)

AF:

0.305

AC:

164083

AN:

538572

Other (OTH)

AF:

0.312

AC:

11925

AN:

38162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

9546

19091

28637

38182

47728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3608

7216

10824

14432

18040

<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:

0.281

AC:

42796

AN:

152172

Hom.:

6327

Cov.:

AF XY:

0.282

AC XY:

21014

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.216

AC:

8984

AN:

41554

American (AMR)

AF:

0.275

AC:

4209

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

1556

AN:

3466

East Asian (EAS)

AF:

0.224

AC:

1152

AN:

5152

South Asian (SAS)

AF:

0.441

AC:

2128

AN:

4826

European-Finnish (FIN)

AF:

0.238

AC:

2524

AN:

10598

Middle Eastern (MID)

AF:

0.373

AC:

109

AN:

292

European-Non Finnish (NFE)

AF:

0.310

AC:

21071

AN:

67970

Other (OTH)

AF:

0.311

AC:

658

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1589

3179

4768

6358

7947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.301

Hom.:

892

Bravo

AF:

0.275

Asia WGS

AF:

0.375

AC:

1301

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.52

(source)

DANN

Benign

0.57

PhyloP100

-0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over