17-3449079-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001170698.2(SPATA22):c.400C>T(p.Arg134*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,230 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001170698.2 stop_gained
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA22 | NM_001170698.2 | c.400C>T | p.Arg134* | stop_gained | 6/9 | ENST00000572969.6 | NP_001164169.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA22 | ENST00000572969.6 | c.400C>T | p.Arg134* | stop_gained | 6/9 | 1 | NM_001170698.2 | ENSP00000460187.1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151762Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250910Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135616
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461350Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 726976
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151880Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74208
ClinVar
Submissions by phenotype
PREMATURE OVARIAN FAILURE 25 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2024 | - - |
SPERMATOGENIC FAILURE 96 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at