dbSNP rs5892: SCARB1:p.Phe301Phe (chr12-124807867-G-A) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_005505.5(SCARB1):c.903C>T(p.Phe301Phe) 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:3

Conservation

PhyloP100: 0.0290

Publications

18 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:

ENSG00000287242 (HGNC:):

ENSG00000287242 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 1224092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
SCARB1	NM_005505.5 link	c.903C>T	p.Phe301Phe	synonymous_variant	Exon 7 of 13	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.903C>T	p.Phe301Phe	synonymous_variant	Exon 7 of 13	1	NM_005505.5	ENSP00000261693.6		Q8WTV0-2

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

GnomAD2 exomes

AF:

0.0177

AC:

4450

AN:

251478

AF XY:

0.0180

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 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

African (AFR)

AF:

0.0780

AC:

2613

AN:

33480

American (AMR)

AF:

0.00713

AC:

319

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0135

AC:

354

AN:

26136

East Asian (EAS)

AF:

0.0284

AC:

1126

AN:

39700

South Asian (SAS)

AF:

0.0424

AC:

3657

AN:

86254

European-Finnish (FIN)

AF:

0.00110

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.0194

AC:

112

AN:

5768

European-Non Finnish (NFE)

AF:

0.00577

AC:

6421

AN:

1111954

Other (OTH)

AF:

0.0186

AC:

1121

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

927

1854

2780

3707

4634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.0261

AC:

3967

AN:

152244

Hom.:

121

Cov.:

AF XY:

0.0264

AC XY:

1963

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0692

AC:

2874

AN:

41544

American (AMR)

AF:

0.00849

AC:

130

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0161

AC:

AN:

3472

East Asian (EAS)

AF:

0.0400

AC:

206

AN:

5156

South Asian (SAS)

AF:

0.0487

AC:

235

AN:

4824

European-Finnish (FIN)

AF:

0.00141

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00575

AC:

391

AN:

68016

Other (OTH)

AF:

0.0237

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

192

384

575

767

959

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0138

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:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Oct 04, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

0.029

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over