chr5-1009550-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033120.4(NKD2):c.131G>A(p.Arg44Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000532 in 1,486,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKD2 | NM_033120.4 | c.131G>A | p.Arg44Gln | missense_variant | 3/10 | ENST00000296849.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.131G>A | p.Arg44Gln | missense_variant | 3/10 | 1 | NM_033120.4 | P2 | |
NKD2 | ENST00000274150.4 | c.131G>A | p.Arg44Gln | missense_variant | 3/11 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 151982Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000382 AC: 51AN: 1334228Hom.: 0 Cov.: 31 AF XY: 0.0000350 AC XY: 23AN XY: 658078
GnomAD4 genome AF: 0.000184 AC: 28AN: 151982Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.131G>A (p.R44Q) alteration is located in exon 3 (coding exon 3) of the NKD2 gene. This alteration results from a G to A substitution at nucleotide position 131, causing the arginine (R) at amino acid position 44 to be replaced by a glutamine (Q). 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