chr17-81902420-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_148896.5(NPB):c.143G>A(p.Arg48His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,351,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_148896.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPB | NM_148896.5 | c.143G>A | p.Arg48His | missense_variant | 1/2 | ENST00000333383.8 | |
PCYT2 | NM_002861.5 | c.*2413C>T | 3_prime_UTR_variant | 13/13 | ENST00000538936.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPB | ENST00000333383.8 | c.143G>A | p.Arg48His | missense_variant | 1/2 | 1 | NM_148896.5 | P1 | |
PCYT2 | ENST00000538936.7 | c.*2413C>T | 3_prime_UTR_variant | 13/13 | 1 | NM_002861.5 | P1 | ||
NPB | ENST00000573081.1 | c.143G>A | p.Arg48His | missense_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000158 AC: 19AN: 1199052Hom.: 0 Cov.: 31 AF XY: 0.0000208 AC XY: 12AN XY: 577442
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2021 | The c.143G>A (p.R48H) alteration is located in exon 1 (coding exon 1) of the NPB gene. This alteration results from a G to A substitution at nucleotide position 143, causing the arginine (R) at amino acid position 48 to be replaced by a histidine (H). 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