19-47500657-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003827.4(NAPA):c.271G>A(p.Ala91Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,610,264 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003827.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAPA | NM_003827.4 | c.271G>A | p.Ala91Thr | missense_variant | Exon 3 of 11 | ENST00000263354.8 | NP_003818.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246496Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133476
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1457900Hom.: 0 Cov.: 30 AF XY: 0.00000965 AC XY: 7AN XY: 725240
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.271G>A (p.A91T) alteration is located in exon 3 (coding exon 3) of the NAPA gene. This alteration results from a G to A substitution at nucleotide position 271, causing the alanine (A) at amino acid position 91 to be replaced by a threonine (T). 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