4-4197434-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_177998.3(OTOP1):c.1400G>A(p.Cys467Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_177998.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251178Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135756
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727240
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1400G>A (p.C467Y) alteration is located in exon 5 (coding exon 5) of the OTOP1 gene. This alteration results from a G to A substitution at nucleotide position 1400, causing the cysteine (C) at amino acid position 467 to be replaced by a tyrosine (Y). 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