chr17-3467540-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001170698.2(SPATA22):c.58C>T(p.Pro20Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000997 in 1,604,512 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P20L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001170698.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA22 | NM_001170698.2 | c.58C>T | p.Pro20Ser | missense_variant | 3/9 | ENST00000572969.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA22 | ENST00000572969.6 | c.58C>T | p.Pro20Ser | missense_variant | 3/9 | 1 | NM_001170698.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000569 AC: 14AN: 246248Hom.: 0 AF XY: 0.0000602 AC XY: 8AN XY: 132994
GnomAD4 exome AF: 0.00000964 AC: 14AN: 1452592Hom.: 0 Cov.: 30 AF XY: 0.00000969 AC XY: 7AN XY: 722204
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.58C>T (p.P20S) alteration is located in exon 3 (coding exon 2) of the SPATA22 gene. This alteration results from a C to T substitution at nucleotide position 58, causing the proline (P) at amino acid position 20 to be replaced by a serine (S). 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