Variant 3-20095467-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003884.5(KAT2B):c.576+59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 1,232,466 control chromosomes in the GnomAD database, including 7,829 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1293 hom., cov: 33)

Exomes 𝑓: 0.088 ( 6536 hom. )

Consequence

KAT2B
NM_003884.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.12

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 Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-20095467-A-G is Benign according to our data. Variant chr3-20095467-A-G is described in ClinVar as [Benign]. Clinvar id is 1248240.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
KAT2B	NM_003884.5 linkuse as main transcript	c.576+59A>G	intron_variant	ENST00000263754.5
KAT2B	XM_005265528.5 linkuse as main transcript	c.576+59A>G	intron_variant
KAT2B	XM_047449147.1 linkuse as main transcript	c.285+59A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT2B	ENST00000263754.5 linkuse as main transcript	c.576+59A>G		intron_variant		1	NM_003884.5	P1
KAT2B	ENST00000426228.1 linkuse as main transcript	n.356+59A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16653

AN:

152116

Hom.:

1289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0634

Gnomad ASJ

AF:

0.0939

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0703

Gnomad OTH

AF:

0.102

GnomAD4 exome

AF:

0.0877

AC:

94769

AN:

1080232

Hom.:

6536

AF XY:

0.0891

AC XY:

48563

AN XY:

545120

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.0788

Gnomad4 ASJ exome

AF:

0.0957

Gnomad4 EAS exome

AF:

0.396

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.0663

Gnomad4 OTH exome

AF:

0.0982

GnomAD4 genome

AF:

0.110

AC:

16679

AN:

152234

Hom.:

1293

Cov.:

AF XY:

0.112

AC XY:

8371

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.0633

Gnomad4 ASJ

AF:

0.0939

Gnomad4 EAS

AF:

0.415

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0703

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0793

Hom.:

1098

Bravo

AF:

0.111

Asia WGS

AF:

0.234

AC:

812

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.038

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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