Variant 3-20072556-G-A 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.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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.00

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=-0.93).

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_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
KAT2B	NM_003884.5 linkuse as main transcript	c.430+97G>A	intron_variant	ENST00000263754.5
KAT2B	XM_005265528.5 linkuse as main transcript	c.430+97G>A	intron_variant
KAT2B	XM_047449147.1 linkuse as main transcript	c.139+97G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT2B	ENST00000263754.5 linkuse as main transcript	c.430+97G>A		intron_variant		1	NM_003884.5	P1
KAT2B	ENST00000426228.1 linkuse as main transcript	n.210+97G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62589

AN:

151708

Hom.:

13178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.491

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.380

AC:

382393

AN:

1005948

Hom.:

73732

AF XY:

0.384

AC XY:

197922

AN XY:

515486

show subpopulations

Gnomad4 AFR exome

AF:

0.482

Gnomad4 AMR exome

AF:

0.388

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.479

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.413

AC:

62652

AN:

151824

Hom.:

13200

Cov.:

AF XY:

0.414

AC XY:

30711

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.491

Gnomad4 AMR

AF:

0.399

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.426

Gnomad4 SAS

AF:

0.494

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.279

Hom.:

766

Bravo

AF:

0.415

Asia WGS

AF:

0.440

AC:

1532

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

-0.93

CADD

Benign

0.0020

DANN

Benign

0.65

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