chrX-68206603-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_002547.3(OPHN1):c.903G>A(p.Thr301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,208,758 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T301T) has been classified as Benign.
Frequency
Consequence
NM_002547.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPHN1 | NM_002547.3 | c.903G>A | p.Thr301= | synonymous_variant | 10/25 | ENST00000355520.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPHN1 | ENST00000355520.6 | c.903G>A | p.Thr301= | synonymous_variant | 10/25 | 1 | NM_002547.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 6AN: 111977Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34167
GnomAD3 exomes AF: 0.0000545 AC: 10AN: 183356Hom.: 0 AF XY: 0.0000885 AC XY: 6AN XY: 67818
GnomAD4 exome AF: 0.0000629 AC: 69AN: 1096781Hom.: 0 Cov.: 29 AF XY: 0.0000773 AC XY: 28AN XY: 362183
GnomAD4 genome AF: 0.0000536 AC: 6AN: 111977Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34167
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 24, 2023 | - - |
OPHN1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 28, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at