chr20-64106713-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005286.4(NPBWR2):c.119C>T(p.Pro40Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,658 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
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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.119C>T | p.Pro40Leu | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.119C>T | p.Pro40Leu | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.119C>T | p.Pro40Leu | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+4158G>A | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+4158G>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249936Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135564
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460464Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 726504
GnomAD4 genome AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2024 | The c.119C>T (p.P40L) alteration is located in exon 1 (coding exon 1) of the NPBWR2 gene. This alteration results from a C to T substitution at nucleotide position 119, causing the proline (P) at amino acid position 40 to be replaced by a leucine (L). 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