Genetic Variant KAT6B:p.Glu1366_Glu1368del (chr10-75028901-GGAAGAGGAA-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_012330.4(KAT6B):c.4097_4105delAAGAGGAAG(p.Glu1366_Glu1368del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0114 in 1,609,368 control chromosomes in the GnomAD database, including 134 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0089 ( 7 hom., cov: 32)

Exomes 𝑓: 0.012 ( 127 hom. )

Consequence

KAT6B
NM_012330.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 3.67

Variant links:

Genes affected

KAT6B (HGNC:17582): (lysine acetyltransferase 6B) The protein encoded by this gene is a histone acetyltransferase and component of the MOZ/MORF protein complex. In addition to its acetyltransferase activity, the encoded protein has transcriptional activation activity in its N-terminal end and transcriptional repression activity in its C-terminal end. This protein is necessary for RUNX2-dependent transcriptional activation and could be involved in brain development. Mutations have been found in patients with genitopatellar syndrome. A translocation of this gene and the CREBBP gene results in acute myeloid leukemias. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]

KAT6B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 10-75028901-GGAAGAGGAA-G is Benign according to our data. Variant chr10-75028901-GGAAGAGGAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 260243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-75028901-GGAAGAGGAA-G is described in Lovd as [Benign]. Variant chr10-75028901-GGAAGAGGAA-G is described in Lovd as [Benign]. Variant chr10-75028901-GGAAGAGGAA-G is described in Lovd as [Likely_benign].

BS2

High AC in GnomAd4 at 1352 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT6B	NM_012330.4 link	c.4097_4105delAAGAGGAAG	p.Glu1366_Glu1368del	disruptive_inframe_deletion	Exon 18 of 18	ENST00000287239.10	NP_036462.2	Q8WYB5-1B2RWN8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT6B	ENST00000287239.10 link	c.4097_4105delAAGAGGAAG	p.Glu1366_Glu1368del	disruptive_inframe_deletion	Exon 18 of 18	1	NM_012330.4	ENSP00000287239.4		Q8WYB5-1

Frequencies

GnomAD3 genomes

AF:

0.00891

AC:

1352

AN:

151686

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00825

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00446

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00405

Gnomad SAS

AF:

0.00270

Gnomad FIN

AF:

0.00227

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.0125

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00750

AC:

1853

AN:

246928

Hom.:

AF XY:

0.00748

AC XY:

1001

AN XY:

133776

show subpopulations

Gnomad AFR exome

AF:

0.00905

Gnomad AMR exome

AF:

0.00336

Gnomad ASJ exome

AF:

0.00430

Gnomad EAS exome

AF:

0.00653

Gnomad SAS exome

AF:

0.00335

Gnomad FIN exome

AF:

0.00212

Gnomad NFE exome

AF:

0.0112

Gnomad OTH exome

AF:

0.00775

GnomAD4 exome

AF:

0.0116

AC:

16978

AN:

1457564

Hom.:

127

AF XY:

0.0113

AC XY:

8188

AN XY:

725230

show subpopulations

Gnomad4 AFR exome

AF:

0.00872

Gnomad4 AMR exome

AF:

0.00364

Gnomad4 ASJ exome

AF:

0.00418

Gnomad4 EAS exome

AF:

0.00660

Gnomad4 SAS exome

AF:

0.00330

Gnomad4 FIN exome

AF:

0.00243

Gnomad4 NFE exome

AF:

0.0137

Gnomad4 OTH exome

AF:

0.00956

GnomAD4 genome

AF:

0.00891

AC:

1352

AN:

151804

Hom.:

Cov.:

AF XY:

0.00845

AC XY:

627

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.00825

Gnomad4 AMR

AF:

0.00445

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00406

Gnomad4 SAS

AF:

0.00270

Gnomad4 FIN

AF:

0.00227

Gnomad4 NFE

AF:

0.0125

Gnomad4 OTH

AF:

0.00711

Alfa

AF:

0.00479

Hom.:

Bravo

AF:

0.00926

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:3

Jan 13, 2016

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 01, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

KAT6B: BS1, BS2 -

Genitopatellar syndrome

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 28, 2019

Mendelics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

10-75028901-GGAAGAGGAAGAAGAGGAA-GGAAGAGGAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over