5-1009502-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033120.4(NKD2):c.83C>T(p.Ala28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000294 in 1,498,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033120.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000417 AC: 4AN: 95888Hom.: 0 AF XY: 0.0000555 AC XY: 3AN XY: 54022
GnomAD4 exome AF: 0.0000267 AC: 36AN: 1346192Hom.: 0 Cov.: 31 AF XY: 0.0000301 AC XY: 20AN XY: 664116
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.83C>T (p.A28V) alteration is located in exon 3 (coding exon 3) of the NKD2 gene. This alteration results from a C to T substitution at nucleotide position 83, causing the alanine (A) at amino acid position 28 to be replaced by a valine (V). 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