3-20042389-C-T

Variant names:

• chr3-20042389-C-T
• rs1915919
• NM_003884.5:c.303+1609C>T

Variant summary

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

The NM_003884.5(KAT2B):​c.303+1609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,942 control chromosomes in the GnomAD database, including 11,575 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 0.38 (11575 hom., cov: 32)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003884.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KAT2B	NM_003884.5	MANE Select	c.303+1609C>T		intron	N/A	NP_003875.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KAT2B	ENST00000263754.5	TSL:1 MANE Select	c.303+1609C>T		intron	N/A	ENSP00000263754.4	Q92831
	KAT2B	ENST00000956100.1		c.303+1609C>T		intron	N/A	ENSP00000626159.1
	KAT2B	ENST00000956099.1		c.303+1609C>T		intron	N/A	ENSP00000626158.1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58004 AN: 151824 Hom.: 11571 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.382 AC: 58039 AN: 151942 Hom.: 11575 Cov.: 32 AF XY: 0.372 AC XY: 27648 AN XY: 74240

African (AFR) AF: 0.402 AC: 16647 AN: 41398

American (AMR) AF: 0.337 AC: 5147 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5174

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4824

European-Finnish (FIN) AF: 0.397 AC: 4184 AN: 10538

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28364 AN: 67966

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.395 Hom.: 41426

Bravo AF: 0.378

Asia WGS AF: 0.144 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.48
PhyloP100		-2.1
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: rs1915919; hg19: chr3-20083881;