rs559824889

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_012330.4(KAT6B):c.3310_3312dupGAA(p.Glu1104dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00636 in 1,605,902 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 2 hom., cov: 22)

Exomes 𝑓: 0.0065 ( 19 hom. )

Consequence

KAT6B
NM_012330.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 3.08

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 10-75022147-G-GGAA is Benign according to our data. Variant chr10-75022147-G-GGAA is described in ClinVar as [Likely_benign]. Clinvar id is 260238.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 801 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT6B	NM_012330.4 link	c.3310_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	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_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	Exon 16 of 18	1	NM_012330.4	ENSP00000287239.4		Q8WYB5-1

Frequencies

GnomAD3 genomes

AF:

0.00535

AC:

803

AN:

150036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00146

Gnomad AMI

AF:

0.0881

Gnomad AMR

AF:

0.00697

Gnomad ASJ

AF:

0.00549

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00191

Gnomad FIN

AF:

0.00250

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.00727

Gnomad OTH

AF:

0.00389

GnomAD3 exomes

AF:

0.00505

AC:

1203

AN:

238206

Hom.:

AF XY:

0.00512

AC XY:

664

AN XY:

129600

show subpopulations

Gnomad AFR exome

AF:

0.000946

Gnomad AMR exome

AF:

0.00453

Gnomad ASJ exome

AF:

0.00358

Gnomad EAS exome

AF:

0.000168

Gnomad SAS exome

AF:

0.00201

Gnomad FIN exome

AF:

0.00298

Gnomad NFE exome

AF:

0.00807

Gnomad OTH exome

AF:

0.00455

GnomAD4 exome

AF:

0.00646

AC:

9410

AN:

1455750

Hom.:

Cov.:

AF XY:

0.00649

AC XY:

4704

AN XY:

724420

show subpopulations

Gnomad4 AFR exome

AF:

0.000819

Gnomad4 AMR exome

AF:

0.00426

Gnomad4 ASJ exome

AF:

0.00372

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.00159

Gnomad4 FIN exome

AF:

0.00328

Gnomad4 NFE exome

AF:

0.00760

Gnomad4 OTH exome

AF:

0.00565

GnomAD4 genome

AF:

0.00533

AC:

801

AN:

150152

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

379

AN XY:

73298

show subpopulations

Gnomad4 AFR

AF:

0.00146

Gnomad4 AMR

AF:

0.00696

Gnomad4 ASJ

AF:

0.00549

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.00192

Gnomad4 FIN

AF:

0.00250

Gnomad4 NFE

AF:

0.00728

Gnomad4 OTH

AF:

0.00385

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

KAT6B: BS2 -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 21, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 28, 2017

Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BS1, BS2, BP3; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and is an in-frame deletion/insertion in a repetitive region without a known function. -

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

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genitopatellar syndrome

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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.

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