Variant chr3-20072497-C-A details in Genebe, Genetics Data Aggregator

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+38C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 1,594,146 control chromosomes in the GnomAD database, including 126,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13317 hom., cov: 32)

Exomes 𝑓: 0.39 ( 112913 hom. )

Consequence

KAT2B
NM_003884.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.974

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 3-20072497-C-A is Benign according to our data. Variant chr3-20072497-C-A is described in ClinVar as [Benign]. Clinvar id is 1259575.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
KAT2B	NM_003884.5 link	c.430+38C>A	intron_variant	ENST00000263754.5	NP_003875.3	Q92831
KAT2B	XM_005265528.5 link	c.430+38C>A	intron_variant		XP_005265585.1
KAT2B	XM_047449147.1 link	c.139+38C>A	intron_variant		XP_047305103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAT2B	ENST00000263754.5 link	c.430+38C>A		intron_variant		1	NM_003884.5	ENSP00000263754.4		Q92831
KAT2B	ENST00000426228.1 link	n.210+38C>A		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62817

AN:

151930

Hom.:

13295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.382

GnomAD3 exomes

AF:

0.399

AC:

99675

AN:

249568

Hom.:

20506

AF XY:

0.400

AC XY:

53922

AN XY:

134910

show subpopulations

Gnomad AFR exome

AF:

0.497

Gnomad AMR exome

AF:

0.378

Gnomad ASJ exome

AF:

0.215

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.483

Gnomad FIN exome

AF:

0.399

Gnomad NFE exome

AF:

0.381

Gnomad OTH exome

AF:

0.371

GnomAD4 exome

AF:

0.392

AC:

565342

AN:

1442100

Hom.:

112913

Cov.:

AF XY:

0.394

AC XY:

282920

AN XY:

718148

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.480

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.386

Gnomad4 OTH exome

AF:

0.385

GnomAD4 genome

AF:

0.414

AC:

62880

AN:

152046

Hom.:

13317

Cov.:

AF XY:

0.415

AC XY:

30874

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.492

Gnomad4 AMR

AF:

0.400

Gnomad4 ASJ

AF:

0.206

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.372

Hom.:

2834

Bravo

AF:

0.415

Asia WGS

AF:

0.441

AC:

1536

AN:

3478

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	clinical testing	GeneDx	May 12, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.5

DANN

Benign

0.45

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