1-15101700-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_201628.3(KAZN):c.1705G>A(p.Val569Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000416 in 1,443,692 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_201628.3 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 |
---|---|---|---|---|---|---|---|
KAZN | NM_201628.3 | c.1705G>A | p.Val569Met | missense_variant | 11/15 | ENST00000376030.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAZN | ENST00000376030.7 | c.1705G>A | p.Val569Met | missense_variant | 11/15 | 5 | NM_201628.3 | P2 | |
KAZN | ENST00000636203.1 | c.1969G>A | p.Val657Met | missense_variant | 13/17 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000134 AC: 3AN: 223608Hom.: 0 AF XY: 0.0000167 AC XY: 2AN XY: 119410
GnomAD4 exome AF: 0.00000416 AC: 6AN: 1443692Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1AN XY: 716038
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.1705G>A (p.V569M) alteration is located in exon 11 (coding exon 11) of the KAZN gene. This alteration results from a G to A substitution at nucleotide position 1705, causing the valine (V) at amino acid position 569 to be replaced by a methionine (M). 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