chr13-52144720-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002498.3(NEK3):āc.775C>Gā(p.Arg259Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000969 in 1,613,792 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R259W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002498.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK3 | NM_002498.3 | c.775C>G | p.Arg259Gly | missense_variant | 9/16 | ENST00000610828.5 | |
NEK3 | NM_152720.3 | c.775C>G | p.Arg259Gly | missense_variant | 9/16 | ||
NEK3 | NR_164641.1 | n.887C>G | non_coding_transcript_exon_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK3 | ENST00000610828.5 | c.775C>G | p.Arg259Gly | missense_variant | 9/16 | 1 | NM_002498.3 | P2 | |
NEK3 | ENST00000618534.4 | c.775C>G | p.Arg259Gly | missense_variant | 9/16 | 5 | P2 | ||
NEK3 | ENST00000620675.4 | c.775C>G | p.Arg259Gly | missense_variant | 9/16 | 5 | A2 | ||
NEK3 | ENST00000617054.1 | c.775C>G | p.Arg259Gly | missense_variant, NMD_transcript_variant | 8/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00401 AC: 609AN: 152028Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00131 AC: 327AN: 249188Hom.: 1 AF XY: 0.00106 AC XY: 143AN XY: 135190
GnomAD4 exome AF: 0.000651 AC: 951AN: 1461646Hom.: 12 Cov.: 31 AF XY: 0.000607 AC XY: 441AN XY: 727102
GnomAD4 genome AF: 0.00402 AC: 612AN: 152146Hom.: 3 Cov.: 32 AF XY: 0.00426 AC XY: 317AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at