X-68053662-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002547.3(OPHN1):c.2307G>A(p.Gly769Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,209,447 control chromosomes in the GnomAD database, including 2 homozygotes. There are 130 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., 12 hem., cov: 22)
Exomes 𝑓: 0.00020 ( 2 hom. 118 hem. )
Consequence
OPHN1
NM_002547.3 synonymous
NM_002547.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0760
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant X-68053662-C-T is Benign according to our data. Variant chrX-68053662-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 195674.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-68053662-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.076 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00017 (19/111616) while in subpopulation SAS AF= 0.00683 (18/2636). AF 95% confidence interval is 0.00441. There are 0 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 12 XL gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000170 AC: 19AN: 111561Hom.: 0 Cov.: 22 AF XY: 0.000356 AC XY: 12AN XY: 33747
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GnomAD3 exomes AF: 0.000434 AC: 79AN: 182077Hom.: 1 AF XY: 0.000570 AC XY: 38AN XY: 66665
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GnomAD4 exome AF: 0.000198 AC: 217AN: 1097831Hom.: 2 Cov.: 31 AF XY: 0.000325 AC XY: 118AN XY: 363211
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GnomAD4 genome AF: 0.000170 AC: 19AN: 111616Hom.: 0 Cov.: 22 AF XY: 0.000355 AC XY: 12AN XY: 33812
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 10, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 27, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 01, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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