3-20040616-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003884.5(KAT2B):c.139G>C(p.Gly47Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000381 in 1,312,758 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_003884.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT2B | NM_003884.5 | c.139G>C | p.Gly47Arg | missense_variant | 1/18 | ENST00000263754.5 | |
KAT2B | XM_005265528.5 | c.139G>C | p.Gly47Arg | missense_variant | 1/17 | ||
KAT2B | XM_047449147.1 | c.-357G>C | 5_prime_UTR_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT2B | ENST00000263754.5 | c.139G>C | p.Gly47Arg | missense_variant | 1/18 | 1 | NM_003884.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000668 AC: 1AN: 149768Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000344 AC: 4AN: 1162990Hom.: 0 Cov.: 32 AF XY: 0.00000177 AC XY: 1AN XY: 565296
GnomAD4 genome ? AF: 0.00000668 AC: 1AN: 149768Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73020
ClinVar
Submissions by phenotype
KAT2B-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 23, 2024 | The KAT2B c.139G>C variant is predicted to result in the amino acid substitution p.Gly47Arg. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at