rs77554031
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005505.5(SCARB1):c.83T>C(p.Met28Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,598,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
SCARB1
NM_005505.5 missense
NM_005505.5 missense
Scores
2
4
12
Clinical Significance
Conservation
PhyloP100: 2.58
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.14247423).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.83T>C | p.Met28Thr | missense_variant | 1/13 | ENST00000261693.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB1 | ENST00000261693.11 | c.83T>C | p.Met28Thr | missense_variant | 1/13 | 1 | NM_005505.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152122Hom.: 0 Cov.: 33
GnomAD3 genomes
?
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152122
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33
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GnomAD3 exomes AF: 0.000151 AC: 34AN: 225486Hom.: 0 AF XY: 0.000138 AC XY: 17AN XY: 123012
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GnomAD4 exome AF: 0.000106 AC: 154AN: 1446822Hom.: 0 Cov.: 31 AF XY: 0.000120 AC XY: 86AN XY: 719162
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152122Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74316
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
High density lipoprotein cholesterol level quantitative trait locus 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | May 05, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.;.
MutationTaster
Benign
D;D;D;D;N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N
REVEL
Uncertain
Sift
Uncertain
D;T;D;D;T
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.42, 0.43, 0.28
.;B;B;B;.
Vest4
MutPred
Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP
MPC
0.71
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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