chr14-75084623-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_033116.6(NEK9):c.2881G>A(p.Asp961Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. D961Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_033116.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK9 | NM_033116.6 | c.2881G>A | p.Asp961Asn | missense_variant | 22/22 | ENST00000238616.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK9 | ENST00000238616.10 | c.2881G>A | p.Asp961Asn | missense_variant | 22/22 | 1 | NM_033116.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251318Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135850
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461864Hom.: 0 Cov.: 38 AF XY: 0.00000963 AC XY: 7AN XY: 727234
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74346
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.2881G>A (p.D961N) alteration is located in exon 22 (coding exon 22) of the NEK9 gene. This alteration results from a G to A substitution at nucleotide position 2881, causing the aspartic acid (D) at amino acid position 961 to be replaced by an asparagine (N). 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