3-20053074-T-C

Position:

• chr3-20053074-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003884.5(KAT2B):​c.303+12294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,226 control chromosomes in the GnomAD database, including 55,281 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (55281 hom., cov: 33)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAT2B	NM_003884.5	c.303+12294T>C		intron_variant		ENST00000263754.5
KAT2B	XM_005265528.5	c.303+12294T>C		intron_variant
KAT2B	XM_047449147.1	c.-193+12294T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT2B	ENST00000263754.5	c.303+12294T>C		intron_variant		1	NM_003884.5	P1
KAT2B	ENST00000426228.1	n.83+12294T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129356 AN: 152108 Hom.: 55234 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.821

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.850 AC: 129462 AN: 152226 Hom.: 55281 Cov.: 33 AF XY: 0.854 AC XY: 63538 AN XY: 74432

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.823

Alfa AF: 0.837 Hom.: 9039

Bravo AF: 0.844

Asia WGS AF: 0.928 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs2929404; hg19: chr3-20094566;