1-52927317-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002979.5(SCP2):c.-80A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00781 in 1,276,736 control chromosomes in the GnomAD database, including 550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.035 ( 318 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 232 hom. )
Consequence
SCP2
NM_002979.5 5_prime_UTR
NM_002979.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.00
Genes affected
SCP2 (HGNC:10606): (sterol carrier protein 2) This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]
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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=-0.9).
BP6
?
Variant 1-52927317-A-T is Benign according to our data. Variant chr1-52927317-A-T is described in ClinVar as [Benign]. Clinvar id is 1296645.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCP2 | NM_002979.5 | c.-80A>T | 5_prime_UTR_variant | 1/16 | ENST00000371514.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCP2 | ENST00000371514.8 | c.-80A>T | 5_prime_UTR_variant | 1/16 | 1 | NM_002979.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0350 AC: 5311AN: 151818Hom.: 317 Cov.: 32
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GnomAD4 exome AF: 0.00413 AC: 4643AN: 1124808Hom.: 232 Cov.: 16 AF XY: 0.00361 AC XY: 2044AN XY: 566560
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GnomAD4 genome ? AF: 0.0351 AC: 5326AN: 151928Hom.: 318 Cov.: 32 AF XY: 0.0336 AC XY: 2496AN XY: 74276
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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 | Aug 25, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at