rs492933
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002547.3(OPHN1):c.*3170G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 111,088 control chromosomes in the GnomAD database, including 12,200 homozygotes. There are 15,508 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002547.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPHN1 | NM_002547.3 | c.*3170G>A | 3_prime_UTR_variant | 25/25 | ENST00000355520.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPHN1 | ENST00000355520.6 | c.*3170G>A | 3_prime_UTR_variant | 25/25 | 1 | NM_002547.3 | P1 | ||
OPHN1 | ENST00000679822.1 | c.*3070G>A | 3_prime_UTR_variant | 20/20 | |||||
OPHN1 | ENST00000680612.1 | c.1686+52868G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.488 AC: 54235AN: 111034Hom.: 12185 Cov.: 23 AF XY: 0.465 AC XY: 15451AN XY: 33248
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 3Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 3
GnomAD4 genome ? AF: 0.489 AC: 54312AN: 111088Hom.: 12200 Cov.: 23 AF XY: 0.466 AC XY: 15508AN XY: 33312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at