rs2929408

Variant names:

• chr3-20041477-C-A
• rs2929408
• NM_003884.5:c.303+697C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-20041477-C-A
• chr3-20041477-C-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+697C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,110 control chromosomes in the GnomAD database, including 2,420 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 0.17 (2420 hom., cov: 32)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 5 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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT2B	NM_003884.5	c.303+697C>A		intron_variant	Intron 1 of 17	ENST00000263754.5	NP_003875.3
KAT2B	XM_005265528.5	c.303+697C>A		intron_variant	Intron 1 of 16		XP_005265585.1
KAT2B	XM_047449147.1	c.-193+697C>A		intron_variant	Intron 1 of 19		XP_047305103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT2B	ENST00000263754.5	c.303+697C>A		intron_variant	Intron 1 of 17	1	NM_003884.5	ENSP00000263754.4
KAT2B	ENST00000426228.1	n.83+697C>A		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25152 AN: 151992 Hom.: 2426 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.165 AC: 25162 AN: 152110 Hom.: 2420 Cov.: 32 AF XY: 0.169 AC XY: 12578 AN XY: 74350

African (AFR) AF: 0.111 AC: 4618 AN: 41510

American (AMR) AF: 0.202 AC: 3091 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2344 AN: 5152

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4826

European-Finnish (FIN) AF: 0.160 AC: 1692 AN: 10596

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10851 AN: 67966

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.145 Hom.: 1069

Bravo AF: 0.169

Asia WGS AF: 0.328 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.85
PhyloP100		0.097
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: rs2929408; hg19: chr3-20082969;