chr20-64106113-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.719G>A(p.Arg240Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,611,812 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPBWR2 | NM_005286.4 | c.719G>A | p.Arg240Gln | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.719G>A | p.Arg240Gln | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.719G>A | p.Arg240Gln | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+3558C>T | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+3558C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247212Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134532
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1459558Hom.: 0 Cov.: 36 AF XY: 0.0000193 AC XY: 14AN XY: 726076
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.719G>A (p.R240Q) 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 719, causing the arginine (R) at amino acid position 240 to be replaced by a glutamine (Q). 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