rs2278986
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005505.5(SCARB1):c.426+150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 943,434 control chromosomes in the GnomAD database, including 45,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 6327 hom., cov: 32)
Exomes 𝑓: 0.31 ( 39311 hom. )
Consequence
SCARB1
NM_005505.5 intron
NM_005505.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.187
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 (BayesDel_noAF=-0.91).
BP6
?
Variant 12-124814823-A-G is Benign according to our data. Variant chr12-124814823-A-G is described in ClinVar as [Benign]. Clinvar id is 1242016.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-124814823-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.426+150T>C | intron_variant | ENST00000261693.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB1 | ENST00000261693.11 | c.426+150T>C | intron_variant | 1 | NM_005505.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.281 AC: 42746AN: 152054Hom.: 6312 Cov.: 32
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GnomAD4 exome AF: 0.308 AC: 243487AN: 791262Hom.: 39311 AF XY: 0.316 AC XY: 129676AN XY: 410440
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GnomAD4 genome ? AF: 0.281 AC: 42796AN: 152172Hom.: 6327 Cov.: 32 AF XY: 0.282 AC XY: 21014AN XY: 74388
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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 | Sep 17, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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