chr5-1035404-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_033120.4(NKD2):c.590G>A(p.Arg197His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,558,670 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKD2 | NM_033120.4 | c.590G>A | p.Arg197His | missense_variant | 8/10 | ENST00000296849.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKD2 | ENST00000296849.10 | c.590G>A | p.Arg197His | missense_variant | 8/10 | 1 | NM_033120.4 | P2 | |
NKD2 | ENST00000274150.4 | c.590G>A | p.Arg197His | missense_variant | 8/11 | 1 | A2 | ||
NKD2 | ENST00000519933.5 | n.359G>A | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
NKD2 | ENST00000523688.1 | n.164G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00358 AC: 545AN: 152254Hom.: 3 Cov.: 34
GnomAD3 exomes AF: 0.00392 AC: 662AN: 168944Hom.: 10 AF XY: 0.00357 AC XY: 319AN XY: 89350
GnomAD4 exome AF: 0.00297 AC: 4175AN: 1406298Hom.: 31 Cov.: 33 AF XY: 0.00289 AC XY: 2007AN XY: 694384
GnomAD4 genome AF: 0.00358 AC: 545AN: 152372Hom.: 3 Cov.: 34 AF XY: 0.00435 AC XY: 324AN XY: 74518
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | NKD2: BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at