3-52711826-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003157.6(NEK4):āc.2477G>Cā(p.Ser826Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,611,124 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 (ā ).
Frequency
Consequence
NM_003157.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEK4 | NM_003157.6 | c.2477G>C | p.Ser826Thr | missense_variant | 16/16 | ENST00000233027.10 | NP_003148.2 | |
NEK4 | NM_001348412.2 | c.2339G>C | p.Ser780Thr | missense_variant | 15/15 | NP_001335341.1 | ||
NEK4 | NM_001348414.2 | c.2231G>C | p.Ser744Thr | missense_variant | 16/16 | NP_001335343.1 | ||
NEK4 | NM_001193533.3 | c.2210G>C | p.Ser737Thr | missense_variant | 15/15 | NP_001180462.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458914Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 725830
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2024 | The c.2477G>C (p.S826T) alteration is located in exon 16 (coding exon 16) of the NEK4 gene. This alteration results from a G to C substitution at nucleotide position 2477, causing the serine (S) at amino acid position 826 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