chr17-50549485-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_022827.4(SPATA20):c.860C>T(p.Pro287Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,611,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022827.4 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
SPATA20 | NM_022827.4 | c.860C>T | p.Pro287Leu | missense_variant, splice_region_variant | 7/17 | ENST00000006658.11 | |
SPATA20 | NM_001258372.2 | c.812C>T | p.Pro271Leu | missense_variant, splice_region_variant | 6/16 | ||
SPATA20 | NM_001258373.2 | c.680C>T | p.Pro227Leu | missense_variant, splice_region_variant | 7/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA20 | ENST00000006658.11 | c.860C>T | p.Pro287Leu | missense_variant, splice_region_variant | 7/17 | 1 | NM_022827.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000491 AC: 12AN: 244280Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133308
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1458684Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 725566
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.860C>T (p.P287L) alteration is located in exon 7 (coding exon 7) of the SPATA20 gene. This alteration results from a C to T substitution at nucleotide position 860, causing the proline (P) at amino acid position 287 to be replaced by a leucine (L). 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