Genetic Variant SCARB1:c.*1336C>T (chr12-124777251-G-A) – 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.*1336C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,838 control chromosomes in the GnomAD database, including 29,347 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 0.60 ( 29346 hom., cov: 31)

Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

SCARB1
NM_005505.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839

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:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 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.*1336C>T	3_prime_UTR	Exon 13 of 13	NP_005496.4
SCARB1	NM_001367981.1		c.*1328C>T	3_prime_UTR	Exon 12 of 12	NP_001354910.1	Q8WTV0-1
SCARB1	NM_001367983.1		c.*1336C>T	3_prime_UTR	Exon 13 of 13	NP_001354912.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.*1336C>T	3_prime_UTR	Exon 13 of 13	ENSP00000261693.6	Q8WTV0-2
SCARB1	ENST00000339570.9	TSL:5	c.*1216C>T	3_prime_UTR	Exon 12 of 12	ENSP00000343795.4	Q8WTV0-5
SCARB1	ENST00000680596.1		c.*1216C>T	3_prime_UTR	Exon 12 of 12	ENSP00000505605.1	A0A7P0T9I2

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91518

AN:

151714

Hom.:

29337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.797

Gnomad AMR

AF:

0.740

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.849

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.691

Gnomad OTH

AF:

0.653

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

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:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.603

AC:

91563

AN:

151832

Hom.:

29346

Cov.:

AF XY:

0.602

AC XY:

44677

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.369

AC:

15246

AN:

41354

American (AMR)

AF:

0.740

AC:

11278

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.653

AC:

2266

AN:

3470

East Asian (EAS)

AF:

0.849

AC:

4393

AN:

5172

South Asian (SAS)

AF:

0.603

AC:

2898

AN:

4808

European-Finnish (FIN)

AF:

0.594

AC:

6249

AN:

10512

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.691

AC:

46965

AN:

67964

Other (OTH)

AF:

0.650

AC:

1367

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1615

3230

4845

6460

8075

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.559

Hom.:

2420

Bravo

AF:

0.608

Asia WGS

AF:

0.702

AC:

2441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.28

(source)

DANN

Benign

0.67

PhyloP100

-0.84

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over