rs730086
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021078.3(KAT2A):c.700-21C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,573,456 control chromosomes in the GnomAD database, including 100,910 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 19666 hom., cov: 32)
Exomes 𝑓: 0.33 ( 81244 hom. )
Consequence
KAT2A
NM_021078.3 intron
NM_021078.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.30
Genes affected
KAT2A (HGNC:4201): (lysine acetyltransferase 2A) KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. It also functions as a repressor of NF-kappa-B (see MIM 164011) by promoting ubiquitination of the NF-kappa-B subunit RELA (MIM 164014) in a HAT-independent manner (Mao et al., 2009 [PubMed 19339690]).[supplied by OMIM, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT2A | NM_021078.3 | c.700-21C>T | intron_variant | ENST00000225916.10 | |||
KAT2A | NM_001376227.1 | c.700-21C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT2A | ENST00000225916.10 | c.700-21C>T | intron_variant | 1 | NM_021078.3 | P1 | |||
KAT2A | ENST00000465682.5 | c.454-21C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.453 AC: 68722AN: 151800Hom.: 19618 Cov.: 32
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GnomAD3 exomes AF: 0.330 AC: 72007AN: 217900Hom.: 14116 AF XY: 0.325 AC XY: 38266AN XY: 117628
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GnomAD4 exome AF: 0.326 AC: 463650AN: 1421538Hom.: 81244 Cov.: 31 AF XY: 0.324 AC XY: 227940AN XY: 703644
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GnomAD4 genome ? AF: 0.453 AC: 68827AN: 151918Hom.: 19666 Cov.: 32 AF XY: 0.447 AC XY: 33158AN XY: 74244
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at