chr20-64106672-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005286.4(NPBWR2):c.160G>A(p.Gly54Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,612,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPBWR2 | NM_005286.4 | c.160G>A | p.Gly54Arg | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.160G>A | p.Gly54Arg | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.160G>A | p.Gly54Arg | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+4117C>T | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+4117C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000156 AC: 39AN: 249750Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135474
GnomAD4 exome AF: 0.000116 AC: 170AN: 1460550Hom.: 0 Cov.: 35 AF XY: 0.000145 AC XY: 105AN XY: 726536
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.160G>A (p.G54R) 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 160, causing the glycine (G) at amino acid position 54 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