chr9-124302012-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014397.6(NEK6):c.48C>A(p.Asn16Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000975 in 1,606,512 control chromosomes in the GnomAD database, including 3 homozygotes. 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_014397.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEK6 | NM_014397.6 | c.48C>A | p.Asn16Lys | missense_variant | Exon 2 of 10 | ENST00000320246.10 | NP_055212.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000637 AC: 97AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000534 AC: 127AN: 237686Hom.: 2 AF XY: 0.000467 AC XY: 60AN XY: 128512
GnomAD4 exome AF: 0.00101 AC: 1470AN: 1454218Hom.: 3 Cov.: 30 AF XY: 0.00101 AC XY: 727AN XY: 722622
GnomAD4 genome AF: 0.000637 AC: 97AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.150C>A (p.N50K) alteration is located in exon 3 (coding exon 2) of the NEK6 gene. This alteration results from a C to A substitution at nucleotide position 150, causing the asparagine (N) at amino acid position 50 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