NM_003884.5:c.852-1548C>G

Variant names:

• chr3-20110048-C-G
• rs6776870
• NM_003884.5:c.852-1548C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003884.5(KAT2B):​c.852-1548C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,910 control chromosomes in the GnomAD database, including 2,816 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 0.18 (2816 hom., cov: 31)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT2B	NM_003884.5	c.852-1548C>G		intron_variant	Intron 5 of 17	ENST00000263754.5	NP_003875.3
KAT2B	XM_005265528.5	c.852-1548C>G		intron_variant	Intron 5 of 16		XP_005265585.1
KAT2B	XM_047449147.1	c.561-1548C>G		intron_variant	Intron 7 of 19		XP_047305103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT2B	ENST00000263754.5	c.852-1548C>G		intron_variant	Intron 5 of 17	1	NM_003884.5	ENSP00000263754.4

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28034 AN: 151788 Hom.: 2803 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.0564

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.185 AC: 28066 AN: 151910 Hom.: 2816 Cov.: 31 AF XY: 0.185 AC XY: 13761 AN XY: 74238

African (AFR) AF: 0.177 AC: 7329 AN: 41428

American (AMR) AF: 0.262 AC: 3992 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0564 AC: 195 AN: 3460

East Asian (EAS) AF: 0.317 AC: 1634 AN: 5150

South Asian (SAS) AF: 0.134 AC: 646 AN: 4820

European-Finnish (FIN) AF: 0.169 AC: 1778 AN: 10534

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12042 AN: 67958

Other (OTH) AF: 0.172 AC: 362 AN: 2100

Alfa AF: 0.185 Hom.: 315

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		-0.057
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6776870; hg19: chr3-20151540;