chr12-124786183-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005505.5(SCARB1):c.1401+174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,585,040 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 17 hom., cov: 33)
Exomes 𝑓: 0.00073 ( 20 hom. )
Consequence
SCARB1
NM_005505.5 intron
NM_005505.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.791
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=-0.85).
BP6
?
Variant 12-124786183-A-G is Benign according to our data. Variant chr12-124786183-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1316820.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00645 (982/152330) while in subpopulation AFR AF= 0.0225 (936/41566). AF 95% confidence interval is 0.0213. There are 17 homozygotes in gnomad4. There are 432 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.1401+174T>C | intron_variant | ENST00000261693.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB1 | ENST00000261693.11 | c.1401+174T>C | intron_variant | 1 | NM_005505.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00638 AC: 971AN: 152212Hom.: 13 Cov.: 33
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GnomAD3 exomes AF: 0.00148 AC: 303AN: 205010Hom.: 3 AF XY: 0.00107 AC XY: 122AN XY: 113792
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GnomAD4 exome AF: 0.000728 AC: 1043AN: 1432710Hom.: 20 Cov.: 31 AF XY: 0.000616 AC XY: 439AN XY: 712102
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GnomAD4 genome ? AF: 0.00645 AC: 982AN: 152330Hom.: 17 Cov.: 33 AF XY: 0.00580 AC XY: 432AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 21, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at