19-50358747-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004851.3(NAPSA):c.1069G>T(p.Gly357Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000298 in 1,613,218 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 Uncertain significance (★).
Frequency
Consequence
NM_004851.3 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAPSA | NM_004851.3 | c.1069G>T | p.Gly357Cys | missense_variant | Exon 9 of 9 | ENST00000253719.7 | NP_004842.1 | |
NAPSA | XM_017027512.2 | c.1042G>T | p.Gly348Cys | missense_variant | Exon 9 of 9 | XP_016883001.1 | ||
LOC105372437 | XR_007067299.1 | n.367+6141C>A | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000110 AC: 27AN: 246238Hom.: 0 AF XY: 0.000112 AC XY: 15AN XY: 134030
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461094Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726844
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1069G>T (p.G357C) alteration is located in exon 9 (coding exon 9) of the NAPSA gene. This alteration results from a G to T substitution at nucleotide position 1069, causing the glycine (G) at amino acid position 357 to be replaced by a cysteine (C). 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