8-41932227-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_006766.5(KAT6A):c.5993A>G(p.Asn1998Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000286 in 1,607,592 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 (★). Synonymous variant affecting the same amino acid position (i.e. N1998N) has been classified as Likely benign.
Frequency
Consequence
NM_006766.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6A | NM_006766.5 | c.5993A>G | p.Asn1998Ser | missense_variant | 17/17 | ENST00000265713.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6A | ENST00000265713.8 | c.5993A>G | p.Asn1998Ser | missense_variant | 17/17 | 1 | NM_006766.5 | A2 | |
KAT6A | ENST00000406337.6 | c.5999A>G | p.Asn2000Ser | missense_variant | 18/18 | 5 | A2 | ||
KAT6A | ENST00000396930.4 | c.5993A>G | p.Asn1998Ser | missense_variant | 18/18 | 5 | A2 | ||
KAT6A | ENST00000649817.1 | c.4676A>G | p.Asn1559Ser | missense_variant | 11/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 246138Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 133032
GnomAD4 exome AF: 0.0000289 AC: 42AN: 1455372Hom.: 0 Cov.: 32 AF XY: 0.0000263 AC XY: 19AN XY: 723566
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1998 of the KAT6A protein (p.Asn1998Ser). This variant is present in population databases (rs778809488, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with KAT6A-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at