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GeneBe

rs2070242

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005505.5(SCARB1):c.12C>T(p.Ser4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00527 in 1,529,510 control chromosomes in the GnomAD database, including 353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 194 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 159 hom. )

Consequence

SCARB1
NM_005505.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.396
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 12-124863709-G-A is Benign according to our data. Variant chr12-124863709-G-A is described in ClinVar as [Benign]. Clinvar id is 1283556.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-124863709-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.396 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0931 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCARB1NM_005505.5 linkuse as main transcriptc.12C>T p.Ser4= synonymous_variant 1/13 ENST00000261693.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCARB1ENST00000261693.11 linkuse as main transcriptc.12C>T p.Ser4= synonymous_variant 1/131 NM_005505.5 P3Q8WTV0-2

Frequencies

GnomAD3 genomes
AF:
0.0277
AC:
4217
AN:
152100
Hom.:
194
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0956
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0104
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000620
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.000618
Gnomad OTH
AF:
0.0211
GnomAD3 exomes
AF:
0.00440
AC:
559
AN:
126998
Hom.:
31
AF XY:
0.00329
AC XY:
228
AN XY:
69200
show subpopulations
Gnomad AFR exome
AF:
0.108
Gnomad AMR exome
AF:
0.00456
Gnomad ASJ exome
AF:
0.00188
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000148
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000375
Gnomad OTH exome
AF:
0.00606
GnomAD4 exome
AF:
0.00279
AC:
3838
AN:
1377302
Hom.:
159
Cov.:
31
AF XY:
0.00241
AC XY:
1640
AN XY:
679980
show subpopulations
Gnomad4 AFR exome
AF:
0.103
Gnomad4 AMR exome
AF:
0.00481
Gnomad4 ASJ exome
AF:
0.00228
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000207
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000260
Gnomad4 OTH exome
AF:
0.00646
GnomAD4 genome
AF:
0.0278
AC:
4225
AN:
152208
Hom.:
194
Cov.:
33
AF XY:
0.0267
AC XY:
1987
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.0956
Gnomad4 AMR
AF:
0.0104
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000618
Gnomad4 OTH
AF:
0.0208
Alfa
AF:
0.00916
Hom.:
21
Bravo
AF:
0.0313
Asia WGS
AF:
0.00754
AC:
28
AN:
3464

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxJan 29, 2019- -
SCARB1-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJan 08, 2024This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
Cadd
Benign
7.2
Dann
Benign
0.96
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2070242; hg19: chr12-125348255; API