20-64106039-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005286.4(NPBWR2):c.793G>A(p.Val265Met) variant causes a missense change. The variant allele was found at a frequency of 0.000041 in 1,610,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.793G>A | p.Val265Met | missense_variant | Exon 2 of 2 | NM_005286.4 | ENSP00000508236.1 | |||
NPBWR2 | ENST00000369768.1 | c.793G>A | p.Val265Met | missense_variant | Exon 1 of 1 | 6 | ENSP00000358783.1 | |||
MYT1 | ENST00000659024.1 | c.-313+3484C>T | intron_variant | Intron 1 of 16 | ENSP00000499493.1 | |||||
MYT1 | ENST00000644172.2 | c.22+3484C>T | intron_variant | Intron 1 of 2 | ENSP00000493561.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000972 AC: 24AN: 246970Hom.: 0 AF XY: 0.000142 AC XY: 19AN XY: 134236
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1458634Hom.: 0 Cov.: 36 AF XY: 0.0000634 AC XY: 46AN XY: 725486
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.793G>A (p.V265M) 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 793, causing the valine (V) at amino acid position 265 to be replaced by a methionine (M). 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