chr8-41932225-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP6
The NM_006766.5(KAT6A):c.5995G>A(p.Gly1999Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,451,864 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G1999G) has been classified as Likely benign.
Frequency
Consequence
NM_006766.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6A | NM_006766.5 | c.5995G>A | p.Gly1999Arg | missense_variant | 17/17 | ENST00000265713.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6A | ENST00000265713.8 | c.5995G>A | p.Gly1999Arg | missense_variant | 17/17 | 1 | NM_006766.5 | A2 | |
KAT6A | ENST00000406337.6 | c.6001G>A | p.Gly2001Arg | missense_variant | 18/18 | 5 | A2 | ||
KAT6A | ENST00000396930.4 | c.5995G>A | p.Gly1999Arg | missense_variant | 18/18 | 5 | A2 | ||
KAT6A | ENST00000649817.1 | c.4678G>A | p.Gly1560Arg | missense_variant | 11/11 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243926Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131732
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1451864Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 721444
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2018 | The p.G1999R variant (also known as c.5995G>A), located in coding exon 16 of the KAT6A gene, results from a G to A substitution at nucleotide position 5995. The glycine at codon 1999 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at