3-20072556-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003884.5(KAT2B):c.430+97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 1,157,772 control chromosomes in the GnomAD database, including 86,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.41 ( 13200 hom., cov: 32)
Exomes 𝑓: 0.38 ( 73732 hom. )
Consequence
KAT2B
NM_003884.5 intron
NM_003884.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.00
Genes affected
KAT2B (HGNC:8638): (lysine acetyltransferase 2B) CBP and p300 are large nuclear proteins that bind to many sequence-specific factors involved in cell growth and/or differentiation, including c-jun and the adenoviral oncoprotein E1A. The protein encoded by this gene associates with p300/CBP. It has in vitro and in vivo binding activity with CBP and p300, and competes with E1A for binding sites in p300/CBP. It has histone acetyl transferase activity with core histones and nucleosome core particles, indicating that this protein plays a direct role in transcriptional regulation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 3-20072556-G-A is Benign according to our data. Variant chr3-20072556-G-A is described in ClinVar as [Benign]. Clinvar id is 1287375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KAT2B | NM_003884.5 | c.430+97G>A | intron_variant | ENST00000263754.5 | NP_003875.3 | |||
KAT2B | XM_005265528.5 | c.430+97G>A | intron_variant | XP_005265585.1 | ||||
KAT2B | XM_047449147.1 | c.139+97G>A | intron_variant | XP_047305103.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KAT2B | ENST00000263754.5 | c.430+97G>A | intron_variant | 1 | NM_003884.5 | ENSP00000263754.4 | ||||
KAT2B | ENST00000426228.1 | n.210+97G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.413 AC: 62589AN: 151708Hom.: 13178 Cov.: 32
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GnomAD4 exome AF: 0.380 AC: 382393AN: 1005948Hom.: 73732 AF XY: 0.384 AC XY: 197922AN XY: 515486
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GnomAD4 genome AF: 0.413 AC: 62652AN: 151824Hom.: 13200 Cov.: 32 AF XY: 0.414 AC XY: 30711AN XY: 74158
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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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