X-68052289-C-CA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002547.3(OPHN1):c.2375+250dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 7014 hom., 3376 hem., cov: 0)
Consequence
OPHN1
NM_002547.3 intron
NM_002547.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.11
Genes affected
OPHN1 (HGNC:8148): (oligophrenin 1) This gene encodes a Rho-GTPase-activating protein that promotes GTP hydrolysis of Rho subfamily members. Rho proteins are important mediators of intracellular signal transduction, which affects cell migration and cell morphogenesis. Mutations in this gene are responsible for OPHN1-related X-linked cognitive disability with cerebellar hypoplasia and distinctive facial dysmorhphism. [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-68052289-C-CA is Benign according to our data. Variant chrX-68052289-C-CA is described in ClinVar as [Benign]. Clinvar id is 1243835.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OPHN1 | NM_002547.3 | c.2375+250dupT | intron_variant | ENST00000355520.6 | NP_002538.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OPHN1 | ENST00000355520.6 | c.2375+250dupT | intron_variant | 1 | NM_002547.3 | ENSP00000347710.5 |
Frequencies
GnomAD3 genomes AF: 0.489 AC: 29807AN: 60916Hom.: 7014 Cov.: 0 AF XY: 0.430 AC XY: 3375AN XY: 7850
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.489 AC: 29803AN: 60895Hom.: 7014 Cov.: 0 AF XY: 0.430 AC XY: 3376AN XY: 7851
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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 10, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at