16-1770891-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002513.3(NME3):c.382G>A(p.Glu128Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000368 in 1,577,904 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002513.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NME3 | NM_002513.3 | c.382G>A | p.Glu128Lys | missense_variant | Exon 4 of 5 | ENST00000219302.8 | NP_002504.2 | |
NME3 | XM_005255332.5 | c.382G>A | p.Glu128Lys | missense_variant, splice_region_variant | Exon 4 of 5 | XP_005255389.1 | ||
NME3 | XM_011522503.3 | c.393G>A | p.Ser131Ser | splice_region_variant, synonymous_variant | Exon 4 of 5 | XP_011520805.1 | ||
NME3 | XM_011522504.3 | c.393G>A | p.Ser131Ser | synonymous_variant | Exon 4 of 5 | XP_011520806.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000227 AC: 5AN: 220072Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120714
GnomAD4 exome AF: 0.0000393 AC: 56AN: 1425694Hom.: 0 Cov.: 31 AF XY: 0.0000341 AC XY: 24AN XY: 704004
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.382G>A (p.E128K) alteration is located in exon 4 (coding exon 4) of the NME3 gene. This alteration results from a G to A substitution at nucleotide position 382, causing the glutamic acid (E) at amino acid position 128 to be replaced by a lysine (K). 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