3-20040688-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003884.5(KAT2B):c.211G>A(p.Gly71Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000102 in 1,572,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003884.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT2B | NM_003884.5 | c.211G>A | p.Gly71Ser | missense_variant | 1/18 | ENST00000263754.5 | |
KAT2B | XM_005265528.5 | c.211G>A | p.Gly71Ser | missense_variant | 1/17 | ||
KAT2B | XM_047449147.1 | c.-285G>A | 5_prime_UTR_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT2B | ENST00000263754.5 | c.211G>A | p.Gly71Ser | missense_variant | 1/18 | 1 | NM_003884.5 | P1 | |
KAT2B | ENST00000426228.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151858Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000323 AC: 6AN: 185526Hom.: 0 AF XY: 0.0000380 AC XY: 4AN XY: 105140
GnomAD4 exome AF: 0.00000915 AC: 13AN: 1420464Hom.: 0 Cov.: 32 AF XY: 0.0000113 AC XY: 8AN XY: 706852
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151858Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74140
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.211G>A (p.G71S) alteration is located in exon 1 (coding exon 1) of the KAT2B gene. This alteration results from a G to A substitution at nucleotide position 211, causing the glycine (G) at amino acid position 71 to be replaced by a serine (S). 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