2-63053018-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014562.4(OTX1):c.28T>C(p.Tyr10His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,609,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014562.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTX1 | NM_014562.4 | c.28T>C | p.Tyr10His | missense_variant | Exon 3 of 5 | ENST00000282549.7 | NP_055377.1 | |
OTX1 | NM_001199770.2 | c.28T>C | p.Tyr10His | missense_variant | Exon 3 of 5 | NP_001186699.1 | ||
OTX1 | NR_130153.2 | n.276T>C | non_coding_transcript_exon_variant | Exon 3 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTX1 | ENST00000282549.7 | c.28T>C | p.Tyr10His | missense_variant | Exon 3 of 5 | 1 | NM_014562.4 | ENSP00000282549.2 | ||
OTX1 | ENST00000366671.7 | c.28T>C | p.Tyr10His | missense_variant | Exon 3 of 5 | 3 | ENSP00000355631.3 | |||
OTX1 | ENST00000405984.8 | n.28T>C | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 | ENSP00000385782.4 | ||||
OTX1 | ENST00000484066.2 | n.716T>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457780Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725378
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.28T>C (p.Y10H) alteration is located in exon 3 (coding exon 1) of the OTX1 gene. This alteration results from a T to C substitution at nucleotide position 28, causing the tyrosine (Y) at amino acid position 10 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at