5-1033474-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_033120.4(NKD2):c.305C>T(p.Pro102Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,552,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_033120.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.305C>T | p.Pro102Leu | missense_variant | Exon 5 of 10 | 1 | NM_033120.4 | ENSP00000296849.5 | ||
NKD2 | ENST00000274150.4 | c.305C>T | p.Pro102Leu | missense_variant | Exon 5 of 11 | 1 | ENSP00000274150.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000317 AC: 5AN: 157508Hom.: 0 AF XY: 0.0000359 AC XY: 3AN XY: 83472
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1400542Hom.: 0 Cov.: 31 AF XY: 0.0000145 AC XY: 10AN XY: 691106
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at