chr17-28739168-C-G
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_178170.3(NEK8):c.1384C>G(p.Arg462Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R462Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_178170.3 missense
Scores
Clinical Significance
Conservation
Publications
- renal-hepatic-pancreatic dysplasia 2Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, Ambry Genetics
- autosomal dominant polycystic kidney diseaseInheritance: AD Classification: STRONG Submitted by: ClinGen
- nephronophthisis 9Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- polycystic kidney disease 8Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- nephronophthisis 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- renal-hepatic-pancreatic dysplasiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEK8 | ENST00000268766.11 | c.1384C>G | p.Arg462Gly | missense_variant | Exon 10 of 15 | 1 | NM_178170.3 | ENSP00000268766.6 | ||
NEK8 | ENST00000543014.1 | n.*118+43C>G | intron_variant | Intron 9 of 10 | 2 | ENSP00000465859.1 | ||||
ENSG00000265073 | ENST00000584779.1 | n.417+3181G>C | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.0000119 AC: 3AN: 251488 AF XY: 0.0000147 show subpopulations
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461686Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727166 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at