5-1034271-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_033120.4(NKD2):c.367C>A(p.Arg123Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,540 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R123C) 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.367C>A | p.Arg123Ser | missense_variant | Exon 6 of 10 | 1 | NM_033120.4 | ENSP00000296849.5 | ||
NKD2 | ENST00000274150.4 | c.367C>A | p.Arg123Ser | missense_variant | Exon 6 of 11 | 1 | ENSP00000274150.4 | |||
NKD2 | ENST00000519933.5 | n.136C>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151780Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459760Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726148
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151780Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74136
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at