chr20-23390028-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022080.3(NAPB):c.479C>T(p.Ser160Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022080.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAPB | NM_022080.3 | c.479C>T | p.Ser160Leu | missense_variant, splice_region_variant | 7/11 | ENST00000377026.4 | NP_071363.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAPB | ENST00000377026.4 | c.479C>T | p.Ser160Leu | missense_variant, splice_region_variant | 7/11 | 1 | NM_022080.3 | ENSP00000366225 | P3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250674Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135480
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461596Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727074
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at