10-75022147-GGAA-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_012330.4(KAT6B):c.3310_3312delGAA(p.Glu1104del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.177 in 1,596,330 control chromosomes in the GnomAD database, including 43,575 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 13474 hom., cov: 22)

Exomes 𝑓: 0.16 ( 30101 hom. )

Consequence

KAT6B
NM_012330.4 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 4.43

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:

ENSG00000234149 (HGNC:):

ENSG00000234149 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 10-75022147-GGAA-G is Benign according to our data. Variant chr10-75022147-GGAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 211214.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-75022147-GGAA-G is described in Lovd as [Benign]. Variant chr10-75022147-GGAA-G is described in Lovd as [Likely_benign]. Variant chr10-75022147-GGAA-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT6B	NM_012330.4 link	c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 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.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	1	NM_012330.4	ENSP00000287239.4		Q8WYB5-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

47842

AN:

149910

Hom.:

13423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.0297

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.0842

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.237

AC:

56520

AN:

238206

Hom.:

10195

AF XY:

0.230

AC XY:

29816

AN XY:

129600

show subpopulations

Gnomad AFR exome

AF:

0.755

Gnomad AMR exome

AF:

0.299

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.357

Gnomad SAS exome

AF:

0.401

Gnomad FIN exome

AF:

0.0855

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.162

AC:

234276

AN:

1446304

Hom.:

30101

AF XY:

0.166

AC XY:

119677

AN XY:

719950

show subpopulations

Gnomad4 AFR exome

AF:

0.763

Gnomad4 AMR exome

AF:

0.291

Gnomad4 ASJ exome

AF:

0.164

Gnomad4 EAS exome

AF:

0.387

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.0863

Gnomad4 NFE exome

AF:

0.114

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.320

AC:

47948

AN:

150026

Hom.:

13474

Cov.:

AF XY:

0.317

AC XY:

23218

AN XY:

73242

show subpopulations

Gnomad4 AFR

AF:

0.752

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.356

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.0842

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.274

Bravo

AF:

0.348

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 27, 2015

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: criteria provided, single submitter

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

- -

Aug 14, 2019

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Glu1104del in exon 16 of KAT6B: This variant is is not expected to have clinical significance because it has been identified in 24% (65722/269038) of total chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs12240773). ACMG/AMP Criteria applied: BA1 -

not provided

Benign:3

Jun 08, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 28, 2016

GeneDx

Significance: Benign

Review Status: flagged submission

Collection Method: clinical testing

- -

Nov 29, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Genitopatellar syndrome

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

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