chr17-28728880-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178170.3(NEK8):c.47+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,544,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_178170.3 intron
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
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00000644 AC: 1AN: 155400 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1392670Hom.: 0 Cov.: 29 AF XY: 0.00000145 AC XY: 1AN XY: 687326 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74394 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at