5-1034254-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033120.4(NKD2):c.350C>T(p.Ser117Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,612,140 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.350C>T | p.Ser117Leu | missense_variant | Exon 6 of 10 | 1 | NM_033120.4 | ENSP00000296849.5 | ||
NKD2 | ENST00000274150.4 | c.350C>T | p.Ser117Leu | missense_variant | Exon 6 of 11 | 1 | ENSP00000274150.4 | |||
NKD2 | ENST00000519933.5 | n.119C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248314Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134752
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1459822Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 726124
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.350C>T (p.S117L) alteration is located in exon 6 (coding exon 6) of the NKD2 gene. This alteration results from a C to T substitution at nucleotide position 350, causing the serine (S) at amino acid position 117 to be replaced by a leucine (L). 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