3-20095153-A-T

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.431-110A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 827,244 control chromosomes in the GnomAD database, including 61,578 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.39 (12080 hom., cov: 32)
  • Exomes 𝑓: 0.37 (49498 hom.)
• Consequence: KAT2B NM_003884.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.84

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=-0.94).
• BP6: Variant 3-20095153-A-T is Benign according to our data. Variant chr3-20095153-A-T is described in ClinVar as [Benign]. Clinvar id is 1260901.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAT2B	NM_003884.5	c.431-110A>T		intron_variant		ENST00000263754.5
KAT2B	XM_005265528.5	c.431-110A>T		intron_variant
KAT2B	XM_047449147.1	c.140-110A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT2B	ENST00000263754.5	c.431-110A>T		intron_variant		1	NM_003884.5	P1
KAT2B	ENST00000426228.1	n.211-110A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59288 AN: 151850 Hom.: 12062 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.371 AC: 250616 AN: 675274 Hom.: 49498 AF XY: 0.378 AC XY: 132647 AN XY: 350756

Gnomad4 AFR exome AF: 0.444

Gnomad4 AMR exome AF: 0.401

Gnomad4 ASJ exome AF: 0.326

Gnomad4 EAS exome AF: 0.642

Gnomad4 SAS exome AF: 0.565

Gnomad4 FIN exome AF: 0.371

Gnomad4 NFE exome AF: 0.329

Gnomad4 OTH exome AF: 0.365

GnomAD4 genome AF: 0.391 AC: 59355 AN: 151970 Hom.: 12080 Cov.: 32 AF XY: 0.397 AC XY: 29495 AN XY: 74264

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.366

Alfa AF: 0.365 Hom.: 1286

Bravo AF: 0.392

Asia WGS AF: 0.543 AC: 1890 AN: 3478

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	-0.94
Cadd	Benign	0.0030
Dann	Benign	0.60

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: rs2293141; hg19: chr3-20136645;