3-20040862-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003884.5(KAT2B):c.303+82T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 1,385,482 control chromosomes in the GnomAD database, including 1,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.071 (592 hom., cov: 31)
  • Exomes 𝑓: 0.039 (1368 hom.)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.177

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 3-20040862-T-G is Benign according to our data. Variant chr3-20040862-T-G is described in ClinVar as [Benign]. Clinvar id is 1226690.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAT2B	NM_003884.5	c.303+82T>G		intron_variant		ENST00000263754.5
KAT2B	XM_005265528.5	c.303+82T>G		intron_variant
KAT2B	XM_047449147.1	c.-193+82T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT2B	ENST00000263754.5	c.303+82T>G		intron_variant		1	NM_003884.5	P1
KAT2B	ENST00000426228.1	n.83+82T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0713 AC: 10542 AN: 147808 Hom.: 588 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00339

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0425

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0617

GnomAD4 exome AF: 0.0390 AC: 48322 AN: 1237548 Hom.: 1368 AF XY: 0.0400 AC XY: 24395 AN XY: 609372

Gnomad4 AFR exome AF: 0.161

Gnomad4 AMR exome AF: 0.0243

Gnomad4 ASJ exome AF: 0.0982

Gnomad4 EAS exome AF: 0.0158

Gnomad4 SAS exome AF: 0.0897

Gnomad4 FIN exome AF: 0.0287

Gnomad4 NFE exome AF: 0.0323

Gnomad4 OTH exome AF: 0.0487

GnomAD4 genome AF: 0.0714 AC: 10564 AN: 147934 Hom.: 592 Cov.: 31 AF XY: 0.0700 AC XY: 5061 AN XY: 72254

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0981

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0345

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0150 Hom.: 6

Bravo AF: 0.0727

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	13
Dann	Benign	0.59

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: rs9849842; hg19: chr3-20082354;