chrX-68299002-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_ModerateBP7BS1BS2_Supporting
The NM_002547.3(OPHN1):c.249C>A(p.Ile83Ile) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,151,078 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002547.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000892 AC: 10AN: 112091Hom.: 0 Cov.: 23 AF XY: 0.0000584 AC XY: 2AN XY: 34243
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183172Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67740
GnomAD4 exome AF: 0.0000106 AC: 11AN: 1038987Hom.: 0 Cov.: 20 AF XY: 0.00000946 AC XY: 3AN XY: 317213
GnomAD4 genome AF: 0.0000892 AC: 10AN: 112091Hom.: 0 Cov.: 23 AF XY: 0.0000584 AC XY: 2AN XY: 34243
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at