Variant 3-20040509-GCTGCGGGGCAGGAGCCGGGGCAGGGGCCGGGCCCGGGGCGCTGCCCCCGCAGCCTGCGGCGCTTCCGCCCGCGCCCCCGCAGGGCTCCCCCTGCGCCGCTGCCGCCGGGGGCTCGGGCGC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_003884.5(KAT2B):c.39_158del(p.Ala14_Gly53del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00111 in 1,031,618 control chromosomes in the GnomAD database, including 42 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00022 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0013 ( 41 hom. )

Consequence

KAT2B
NM_003884.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.67

Variant links:

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]

KAT2B links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 3-20040509-GCTGCGGGGCAGGAGCCGGGGCAGGGGCCGGGCCCGGGGCGCTGCCCCCGCAGCCTGCGGCGCTTCCGCCCGCGCCCCCGCAGGGCTCCCCCTGCGCCGCTGCCGCCGGGGGCTCGGGCGC-G is Benign according to our data. Variant chr3-20040509-GCTGCGGGGCAGGAGCCGGGGCAGGGGCCGGGCCCGGGGCGCTGCCCCCGCAGCCTGCGGCGCTTCCGCCCGCGCCCCCGCAGGGCTCCCCCTGCGCCGCTGCCGCCGGGGGCTCGGGCGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3044350.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 33 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KAT2B	NM_003884.5 link	c.39_158del	p.Ala14_Gly53del	disruptive_inframe_deletion	1/18	ENST00000263754.5	NP_003875.3	Q92831
KAT2B	XM_005265528.5 link	c.39_158del	p.Ala14_Gly53del	disruptive_inframe_deletion	1/17		XP_005265585.1
KAT2B	XM_047449147.1 link	c.-457_-338del		5_prime_UTR_variant	1/20		XP_047305103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAT2B	ENST00000263754.5 link	c.39_158del	p.Ala14_Gly53del	disruptive_inframe_deletion	1/18	1	NM_003884.5	ENSP00000263754.4		Q92831

Frequencies

GnomAD3 genomes

AF:

0.000225

AC:

AN:

146972

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000734

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.000270

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00116

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000227

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00126

AC:

1111

AN:

884546

Hom.:

AF XY:

0.00129

AC XY:

533

AN XY:

412902

show subpopulations

Gnomad4 AFR exome

AF:

0.000704

Gnomad4 AMR exome

AF:

0.00954

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000283

Gnomad4 FIN exome

AF:

0.0134

Gnomad4 NFE exome

AF:

0.00115

Gnomad4 OTH exome

AF:

0.00259

GnomAD4 genome

AF:

0.000224

AC:

AN:

147072

Hom.:

Cov.:

AF XY:

0.000168

AC XY:

AN XY:

71620

show subpopulations

Gnomad4 AFR

AF:

0.0000732

Gnomad4 AMR

AF:

0.000270

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00116

Gnomad4 NFE

AF:

0.000227

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000447

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KAT2B-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 19, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over