20-23390261-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022080.3(NAPB):c.424A>G(p.Ile142Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,609,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022080.3 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 | UniProt |
---|---|---|---|---|---|---|---|
NAPB | NM_022080.3 | c.424A>G | p.Ile142Val | missense_variant | 6/11 | ENST00000377026.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAPB | ENST00000377026.4 | c.424A>G | p.Ile142Val | missense_variant | 6/11 | 1 | NM_022080.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250792Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135564
GnomAD4 exome AF: 0.000121 AC: 177AN: 1457358Hom.: 0 Cov.: 29 AF XY: 0.000134 AC XY: 97AN XY: 725314
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74392
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.424A>G (p.I142V) alteration is located in exon 6 (coding exon 6) of the NAPB gene. This alteration results from a A to G substitution at nucleotide position 424, causing the isoleucine (I) at amino acid position 142 to be replaced by a valine (V). 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