chr9-124312522-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014397.6(NEK6):c.104C>T(p.Thr35Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,778 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T35A) has been classified as Likely benign.
Frequency
Consequence
NM_014397.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEK6 | NM_014397.6 | c.104C>T | p.Thr35Met | missense_variant | Exon 3 of 10 | ENST00000320246.10 | NP_055212.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250802Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135604
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461554Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727068
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.206C>T (p.T69M) alteration is located in exon 4 (coding exon 3) of the NEK6 gene. This alteration results from a C to T substitution at nucleotide position 206, causing the threonine (T) at amino acid position 69 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