3-131349675-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024800.5(NEK11):c.1837C>T(p.Pro613Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024800.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251162Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135722
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727232
GnomAD4 genome AF: 0.000217 AC: 33AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1837C>T (p.P613S) alteration is located in exon 18 (coding exon 16) of the NEK11 gene. This alteration results from a C to T substitution at nucleotide position 1837, causing the proline (P) at amino acid position 613 to be replaced by a serine (S). 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