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12-124778515-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005505.5(SCARB1):c.*72G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0174 in 1,230,548 control chromosomes in the GnomAD database, including 3,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 512 hom., cov: 33)
Exomes 𝑓: 0.016 ( 2941 hom. )

Consequence

SCARB1
NM_005505.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.08
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 12-124778515-C-T is Benign according to our data. Variant chr12-124778515-C-T is described in ClinVar as [Benign]. Clinvar id is 1181016.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-124778515-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCARB1NM_005505.5 linkuse as main transcriptc.*72G>A 3_prime_UTR_variant 13/13 ENST00000261693.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCARB1ENST00000261693.11 linkuse as main transcriptc.*72G>A 3_prime_UTR_variant 13/131 NM_005505.5 P3Q8WTV0-2

Frequencies

GnomAD3 genomes
AF:
0.0302
AC:
4557
AN:
150788
Hom.:
512
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00458
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.125
Gnomad ASJ
AF:
0.00289
Gnomad EAS
AF:
0.393
Gnomad SAS
AF:
0.0323
Gnomad FIN
AF:
0.00915
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00216
Gnomad OTH
AF:
0.0371
GnomAD3 exomes
AF:
0.0250
AC:
661
AN:
26458
Hom.:
82
AF XY:
0.0239
AC XY:
317
AN XY:
13238
show subpopulations
Gnomad AFR exome
AF:
0.00278
Gnomad AMR exome
AF:
0.143
Gnomad ASJ exome
AF:
0.00255
Gnomad EAS exome
AF:
0.415
Gnomad SAS exome
AF:
0.0227
Gnomad FIN exome
AF:
0.00993
Gnomad NFE exome
AF:
0.00313
Gnomad OTH exome
AF:
0.0308
GnomAD4 exome
AF:
0.0155
AC:
16786
AN:
1079628
Hom.:
2941
Cov.:
32
AF XY:
0.0156
AC XY:
8109
AN XY:
521334
show subpopulations
Gnomad4 AFR exome
AF:
0.00242
Gnomad4 AMR exome
AF:
0.169
Gnomad4 ASJ exome
AF:
0.00292
Gnomad4 EAS exome
AF:
0.462
Gnomad4 SAS exome
AF:
0.0188
Gnomad4 FIN exome
AF:
0.00973
Gnomad4 NFE exome
AF:
0.000948
Gnomad4 OTH exome
AF:
0.0293
GnomAD4 genome
AF:
0.0302
AC:
4565
AN:
150920
Hom.:
512
Cov.:
33
AF XY:
0.0348
AC XY:
2568
AN XY:
73710
show subpopulations
Gnomad4 AFR
AF:
0.00456
Gnomad4 AMR
AF:
0.125
Gnomad4 ASJ
AF:
0.00289
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.0321
Gnomad4 FIN
AF:
0.00915
Gnomad4 NFE
AF:
0.00216
Gnomad4 OTH
AF:
0.0386
Alfa
AF:
0.0254
Hom.:
159
Bravo
AF:
0.0396
Asia WGS
AF:
0.154
AC:
535
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxOct 17, 2018- -
SCARB1-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 08, 2019This 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
-0.77
Cadd
Benign
0.24
Dann
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs3825140; hg19: chr12-125263061; COSMIC: COSV55552447; COSMIC: COSV55552447; API