chr20-64105931-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005286.4(NPBWR2):āc.901A>Gā(p.Ile301Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,612,682 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005286.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPBWR2 | NM_005286.4 | c.901A>G | p.Ile301Val | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.901A>G | p.Ile301Val | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.901A>G | p.Ile301Val | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+3376T>C | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+3376T>C | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152008Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000268 AC: 67AN: 250166Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135642
GnomAD4 exome AF: 0.000132 AC: 193AN: 1460674Hom.: 2 Cov.: 35 AF XY: 0.000145 AC XY: 105AN XY: 726636
GnomAD4 genome AF: 0.000151 AC: 23AN: 152008Hom.: 0 Cov.: 31 AF XY: 0.000202 AC XY: 15AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.901A>G (p.I301V) alteration is located in exon 1 (coding exon 1) of the NPBWR2 gene. This alteration results from a A to G substitution at nucleotide position 901, causing the isoleucine (I) at amino acid position 301 to be replaced by a valine (V). 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