chr17-50552097-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022827.4(SPATA20):c.1874A>T(p.Lys625Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022827.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA20 | NM_022827.4 | c.1874A>T | p.Lys625Met | missense_variant | 14/17 | ENST00000006658.11 | NP_073738.2 | |
SPATA20 | NM_001258372.2 | c.1826A>T | p.Lys609Met | missense_variant | 13/16 | NP_001245301.1 | ||
SPATA20 | NM_001258373.2 | c.1694A>T | p.Lys565Met | missense_variant | 14/17 | NP_001245302.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA20 | ENST00000006658.11 | c.1874A>T | p.Lys625Met | missense_variant | 14/17 | 1 | NM_022827.4 | ENSP00000006658 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 59
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at