X-48523711-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006579.3(EBP):c.-43del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0038 (0 hom., 30 hem., cov: 0)
  • Exomes 𝑓: 0.18 (3 hom. 48 hem.)
• Consequence: EBP NM_006579.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-48523711-CT-C is Benign according to our data. Variant chrX-48523711-CT-C is described in ClinVar as [Benign]. Clinvar id is 516179.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBP	NM_006579.3	c.-43del		5_prime_UTR_variant	2/5	ENST00000495186.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBP	ENST00000495186.6	c.-43del		5_prime_UTR_variant	2/5	1	NM_006579.3	P1

Frequencies

GnomAD3 genomes AF: 0.00372 AC: 326 AN: 87629 Hom.: 0 Cov.: 0 AF XY: 0.00143 AC XY: 28 AN XY: 19533

Gnomad AFR AF: 0.00697

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00201

Gnomad ASJ AF: 0.000859

Gnomad EAS AF: 0.00217

Gnomad SAS AF: 0.00223

Gnomad FIN AF: 0.00967

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00229

Gnomad OTH AF: 0.00519

GnomAD4 exome AF: 0.180 AC: 119250 AN: 661077 Hom.: 3 Cov.: 0 AF XY: 0.000369 AC XY: 48 AN XY: 130125

Gnomad4 AFR exome AF: 0.189

Gnomad4 AMR exome AF: 0.172

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.187

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.00376 AC: 329 AN: 87604 Hom.: 0 Cov.: 0 AF XY: 0.00154 AC XY: 30 AN XY: 19540

Gnomad4 AFR AF: 0.00705

Gnomad4 AMR AF: 0.00214

Gnomad4 ASJ AF: 0.000859

Gnomad4 EAS AF: 0.00218

Gnomad4 SAS AF: 0.00226

Gnomad4 FIN AF: 0.00967

Gnomad4 NFE AF: 0.00229

Gnomad4 OTH AF: 0.00515

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 04, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs782299900; hg19: chrX-48382099;