17-42117919-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021078.3(KAT2A):c.1279G>A(p.Glu427Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000811 in 1,603,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021078.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KAT2A | NM_021078.3 | c.1279G>A | p.Glu427Lys | missense_variant | Exon 8 of 18 | ENST00000225916.10 | NP_066564.2 | |
KAT2A | NM_001376227.1 | c.1279G>A | p.Glu427Lys | missense_variant | Exon 8 of 18 | NP_001363156.1 | ||
KAT2A | XM_006721818.5 | c.196G>A | p.Glu66Lys | missense_variant | Exon 3 of 13 | XP_006721881.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KAT2A | ENST00000225916.10 | c.1279G>A | p.Glu427Lys | missense_variant | Exon 8 of 18 | 1 | NM_021078.3 | ENSP00000225916.5 | ||
KAT2A | ENST00000465682.5 | n.*393G>A | non_coding_transcript_exon_variant | Exon 8 of 18 | 5 | ENSP00000468390.1 | ||||
KAT2A | ENST00000465682.5 | n.*393G>A | 3_prime_UTR_variant | Exon 8 of 18 | 5 | ENSP00000468390.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242664Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130874
GnomAD4 exome AF: 0.00000827 AC: 12AN: 1451620Hom.: 0 Cov.: 32 AF XY: 0.00000694 AC XY: 5AN XY: 720702
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1279G>A (p.E427K) alteration is located in exon 8 (coding exon 8) of the KAT2A gene. This alteration results from a G to A substitution at nucleotide position 1279, causing the glutamic acid (E) at amino acid position 427 to be replaced by a lysine (K). 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