10-101064420-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_030929.5(KAZALD1):āc.671A>Gā(p.Gln224Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030929.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAZALD1 | NM_030929.5 | c.671A>G | p.Gln224Arg | missense_variant, splice_region_variant | 3/5 | ENST00000370200.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAZALD1 | ENST00000370200.6 | c.671A>G | p.Gln224Arg | missense_variant, splice_region_variant | 3/5 | 1 | NM_030929.5 | P1 | |
KAZALD1 | ENST00000477267.1 | n.186A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | 5 | ||||
KAZALD1 | ENST00000477979.5 | n.327A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251286Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135816
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461868Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727234
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 15, 2021 | The p.Gln224Arg variant, to our knowledge, has not been reported in the medical literature or gene specific databases. Based on the available information, the clinical significance of this variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at