chr1-1757129-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001198994.2(NADK):c.757G>A(p.Ala253Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,540,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001198994.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NADK | NM_023018.5 | c.393+52G>A | intron_variant | Intron 4 of 11 | ENST00000341426.9 | NP_075394.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000922 AC: 14AN: 151906Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000711 AC: 11AN: 154624Hom.: 0 AF XY: 0.0000599 AC XY: 5AN XY: 83482
GnomAD4 exome AF: 0.000188 AC: 261AN: 1388684Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 120AN XY: 684982
GnomAD4 genome AF: 0.0000922 AC: 14AN: 151906Hom.: 0 Cov.: 31 AF XY: 0.0000809 AC XY: 6AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.757G>A (p.A253T) alteration is located in exon 6 (coding exon 5) of the NADK gene. This alteration results from a G to A substitution at nucleotide position 757, causing the alanine (A) at amino acid position 253 to be replaced by a threonine (T). 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