20-64106348-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005286.4(NPBWR2):c.484G>A(p.Gly162Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,784 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005286.4 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 |
---|---|---|---|---|---|---|---|
NPBWR2 | NM_005286.4 | c.484G>A | p.Gly162Arg | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.484G>A | p.Gly162Arg | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.484G>A | p.Gly162Arg | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+3793C>T | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+3793C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000932 AC: 23AN: 246884Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134764
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460456Hom.: 1 Cov.: 35 AF XY: 0.0000619 AC XY: 45AN XY: 726522
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.484G>A (p.G162R) alteration is located in exon 1 (coding exon 1) of the NPBWR2 gene. This alteration results from a G to A substitution at nucleotide position 484, causing the glycine (G) at amino acid position 162 to be replaced by an arginine (R). 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