chr20-64105975-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005286.4(NPBWR2):c.857C>T(p.Thr286Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,612,490 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.857C>T | p.Thr286Met | missense_variant | 2/2 | ENST00000684052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPBWR2 | ENST00000684052.1 | c.857C>T | p.Thr286Met | missense_variant | 2/2 | NM_005286.4 | P1 | ||
NPBWR2 | ENST00000369768.1 | c.857C>T | p.Thr286Met | missense_variant | 1/1 | P1 | |||
MYT1 | ENST00000644172.2 | c.22+3420G>A | intron_variant | ||||||
MYT1 | ENST00000659024.1 | c.-313+3420G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249696Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135426
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1460400Hom.: 0 Cov.: 36 AF XY: 0.0000399 AC XY: 29AN XY: 726462
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.857C>T (p.T286M) 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 857, causing the threonine (T) at amino acid position 286 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