X-68048441-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002547.3(OPHN1):c.2392C>T(p.Pro798Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,096,754 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002547.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OPHN1 | NM_002547.3 | c.2392C>T | p.Pro798Ser | missense_variant | 24/25 | ENST00000355520.6 | NP_002538.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OPHN1 | ENST00000355520.6 | c.2392C>T | p.Pro798Ser | missense_variant | 24/25 | 1 | NM_002547.3 | ENSP00000347710.5 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 0.00000821 AC: 9AN: 1096754Hom.: 0 Cov.: 28 AF XY: 0.0000166 AC XY: 6AN XY: 362182
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2023 | The c.2392C>T (p.P798S) alteration is located in exon 24 (coding exon 23) of the OPHN1 gene. This alteration results from a C to T substitution at nucleotide position 2392, causing the proline (P) at amino acid position 798 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
OPHN1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2023 | The OPHN1 c.2392C>T variant is predicted to result in the amino acid substitution p.Pro798Ser. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.