chr12-124778493-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005505.5(SCARB1):c.*94G>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 0.0106 in 1,348,458 control chromosomes in the GnomAD database, including 1,264 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.054 ( 789 hom., cov: 33)
Exomes 𝑓: 0.0051 ( 475 hom. )
Consequence
SCARB1
NM_005505.5 3_prime_UTR
NM_005505.5 3_prime_UTR
Scores
14
Clinical Significance
Conservation
PhyloP100: -0.743
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0046088696).
BP6
?
Variant 12-124778493-C-T is Benign according to our data. Variant chr12-124778493-C-T is described in ClinVar as [Benign]. Clinvar id is 1297808.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124778493-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.*94G>A | 3_prime_UTR_variant | 13/13 | ENST00000261693.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB1 | ENST00000261693.11 | c.*94G>A | 3_prime_UTR_variant | 13/13 | 1 | NM_005505.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0539 AC: 8192AN: 151954Hom.: 785 Cov.: 33
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GnomAD3 exomes AF: 0.0140 AC: 424AN: 30328Hom.: 40 AF XY: 0.0113 AC XY: 169AN XY: 14890
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GnomAD4 exome AF: 0.00510 AC: 6101AN: 1196384Hom.: 475 Cov.: 32 AF XY: 0.00450 AC XY: 2596AN XY: 576648
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GnomAD4 genome ? AF: 0.0541 AC: 8227AN: 152074Hom.: 789 Cov.: 33 AF XY: 0.0525 AC XY: 3906AN XY: 74342
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ESP6500AA
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644
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ExAC
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1227
Asia WGS
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29
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2019 | This variant is associated with the following publications: (PMID: 27651445) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MutPred
Gain of glycosylation at P497 (P = 0.071);
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at