chrX-48523730-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006579.3(EBP):c.-42A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00081 ( 0 hom., 0 hem., cov: 8)
Exomes 𝑓: 0.00049 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
EBP
NM_006579.3 5_prime_UTR
NM_006579.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.342
Genes affected
EBP (HGNC:3133): (EBP cholestenol delta-isomerase) The protein encoded by this gene is an integral membrane protein of the endoplasmic reticulum. It is a high affinity binding protein for the antiischemic phenylalkylamine Ca2+ antagonist [3H]emopamil and the photoaffinity label [3H]azidopamil. It is similar to sigma receptors and may be a member of a superfamily of high affinity drug-binding proteins in the endoplasmic reticulum of different tissues. This protein shares structural features with bacterial and eukaryontic drug transporting proteins. It has four putative transmembrane segments and contains two conserved glutamate residues which may be involved in the transport of cationic amphiphilics. Another prominent feature of this protein is its high content of aromatic amino acid residues (>23%) in its transmembrane segments. These aromatic amino acid residues have been suggested to be involved in the drug transport by the P-glycoprotein. Mutations in this gene cause Chondrodysplasia punctata 2 (CDPX2; also known as Conradi-Hunermann syndrome). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant X-48523730-A-T is Benign according to our data. Variant chrX-48523730-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1191185.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.-42A>T | 5_prime_UTR_variant | 2/5 | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.-42A>T | 5_prime_UTR_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 38AN: 46940Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 12960 FAILED QC
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GnomAD3 exomes AF: 0.00792 AC: 398AN: 50230Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 16462
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000485 AC: 423AN: 871848Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 246320
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000810 AC: 38AN: 46921Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 12979
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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 | Jul 09, 2018 | - - |
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