chrX-48523711-C-CTTTTT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_006579.3(EBP):c.-47_-43dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.018 ( 21 hom., 201 hem., cov: 0)
Exomes 𝑓: 0.0031 ( 1 hom. 34 hem. )
Consequence
EBP
NM_006579.3 5_prime_UTR
NM_006579.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.474
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 Benign. Variant got -10 ACMG points.
BP6
Variant X-48523711-C-CTTTTT is Benign according to our data. Variant chrX-48523711-C-CTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 1199761.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0181 (1586/87585) while in subpopulation NFE AF= 0.0274 (1232/45017). AF 95% confidence interval is 0.0261. There are 21 homozygotes in gnomad4. There are 201 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 21 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.-47_-43dup | 5_prime_UTR_variant | 2/5 | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.-47_-43dup | 5_prime_UTR_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 1587AN: 87610Hom.: 21 Cov.: 0 AF XY: 0.0103 AC XY: 201AN XY: 19544
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GnomAD4 exome AF: 0.00312 AC: 2398AN: 768768Hom.: 1 Cov.: 0 AF XY: 0.000152 AC XY: 34AN XY: 223756
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GnomAD4 genome AF: 0.0181 AC: 1586AN: 87585Hom.: 21 Cov.: 0 AF XY: 0.0103 AC XY: 201AN XY: 19551
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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 | Dec 13, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at