5-1035391-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033120.4(NKD2):āc.577C>Gā(p.Arg193Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000128 in 1,556,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. 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. R193Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_033120.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.577C>G | p.Arg193Gly | missense_variant, splice_region_variant | Exon 8 of 10 | 1 | NM_033120.4 | ENSP00000296849.5 | ||
NKD2 | ENST00000274150.4 | c.577C>G | p.Arg193Gly | missense_variant, splice_region_variant | Exon 8 of 11 | 1 | ENSP00000274150.4 | |||
NKD2 | ENST00000519933.5 | n.346C>G | splice_region_variant, non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
NKD2 | ENST00000523688.1 | n.151C>G | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 34
GnomAD4 exome AF: 7.12e-7 AC: 1AN: 1404494Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1AN XY: 693254
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at