chrX-48523553-G-GA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_006579.3(EBP):c.-73-129dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 220,936 control chromosomes in the GnomAD database, including 63 homozygotes. There are 310 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.054 ( 55 hom., 254 hem., cov: 19)
Exomes 𝑓: 0.28 ( 8 hom. 56 hem. )
Consequence
EBP
NM_006579.3 intron
NM_006579.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.234
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant X-48523553-G-GA is Benign according to our data. Variant chrX-48523553-G-GA is described in ClinVar as [Benign]. Clinvar id is 1293795.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.071 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.-73-129dup | intron_variant | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.-73-129dup | intron_variant | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0539 AC: 2493AN: 46256Hom.: 55 Cov.: 19 AF XY: 0.0287 AC XY: 254AN XY: 8850
GnomAD3 genomes
?
AF:
AC:
2493
AN:
46256
Hom.:
Cov.:
19
AF XY:
AC XY:
254
AN XY:
8850
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.283 AC: 49368AN: 174674Hom.: 8 AF XY: 0.00209 AC XY: 56AN XY: 26822
GnomAD4 exome
AF:
AC:
49368
AN:
174674
Hom.:
AF XY:
AC XY:
56
AN XY:
26822
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0539 AC: 2492AN: 46262Hom.: 55 Cov.: 19 AF XY: 0.0287 AC XY: 254AN XY: 8856
GnomAD4 genome
?
AF:
AC:
2492
AN:
46262
Hom.:
Cov.:
19
AF XY:
AC XY:
254
AN XY:
8856
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Oct 06, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at