Variant 3-20072338-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_003884.5(KAT2B):c.309G>A(p.Glu103Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,610,800 control chromosomes in the GnomAD database, including 128,207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13309 hom., cov: 31)

Exomes 𝑓: 0.39 ( 114898 hom. )

Consequence

KAT2B
NM_003884.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.375

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:

KAT2B (HGNC:):

KAT2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 3-20072338-G-A is Benign according to our data. Variant chr3-20072338-G-A is described in ClinVar as [Benign]. Clinvar id is 1258558.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.375 with no splicing effect.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KAT2B	NM_003884.5 linkuse as main transcript	c.309G>A	p.Glu103Glu	synonymous_variant	2/18	ENST00000263754.5	NP_003875.3	Q92831
KAT2B	XM_005265528.5 linkuse as main transcript	c.309G>A	p.Glu103Glu	synonymous_variant	2/17		XP_005265585.1
KAT2B	XM_047449147.1 linkuse as main transcript	c.18G>A	p.Glu6Glu	synonymous_variant	4/20		XP_047305103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAT2B	ENST00000263754.5 linkuse as main transcript	c.309G>A	p.Glu103Glu	synonymous_variant	2/18	1	NM_003884.5	ENSP00000263754.4		Q92831
KAT2B	ENST00000426228.1 linkuse as main transcript	n.89G>A		non_coding_transcript_exon_variant	2/5	4

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62760

AN:

151760

Hom.:

13286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.401

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.381

GnomAD3 exomes

AF:

0.399

AC:

100318

AN:

251290

Hom.:

20649

AF XY:

0.400

AC XY:

54264

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.497

Gnomad AMR exome

AF:

0.379

Gnomad ASJ exome

AF:

0.215

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.483

Gnomad FIN exome

AF:

0.398

Gnomad NFE exome

AF:

0.381

Gnomad OTH exome

AF:

0.372

GnomAD4 exome

AF:

0.393

AC:

574001

AN:

1458922

Hom.:

114898

Cov.:

AF XY:

0.395

AC XY:

286888

AN XY:

725892

show subpopulations

Gnomad4 AFR exome

AF:

0.496

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.481

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.387

Gnomad4 OTH exome

AF:

0.386

GnomAD4 genome

AF:

0.414

AC:

62825

AN:

151878

Hom.:

13309

Cov.:

AF XY:

0.415

AC XY:

30829

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.401

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.377

Alfa

AF:

0.369

Hom.:

7651

Bravo

AF:

0.415

Asia WGS

AF:

0.441

AC:

1535

AN:

3478

EpiCase

AF:

0.365

EpiControl

AF:

0.355

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	Sep 01, 2019	- -
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

-0.40

CADD

Benign

8.0

DANN

Benign

0.52

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