chr5-1035392-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033120.4(NKD2):c.578G>A(p.Arg193Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000899 in 1,557,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R193W) has been classified as Uncertain significance.
Frequency
Consequence
NM_033120.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKD2 | NM_033120.4 | c.578G>A | p.Arg193Gln | missense_variant | 8/10 | ENST00000296849.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.578G>A | p.Arg193Gln | missense_variant | 8/10 | 1 | NM_033120.4 | P2 | |
NKD2 | ENST00000274150.4 | c.578G>A | p.Arg193Gln | missense_variant | 8/11 | 1 | A2 | ||
NKD2 | ENST00000519933.5 | n.347G>A | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
NKD2 | ENST00000523688.1 | n.152G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000240 AC: 4AN: 166854Hom.: 0 AF XY: 0.0000227 AC XY: 2AN XY: 88106
GnomAD4 exome AF: 0.00000854 AC: 12AN: 1404818Hom.: 0 Cov.: 32 AF XY: 0.00000721 AC XY: 5AN XY: 693448
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at