10-75022147-GGAA-G

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]

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
KAT6BNM_012330.4 linkc.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
KAT6BENST00000287239.10 linkc.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.:
22
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.:
22
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
-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
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

- -

-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
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
Nov 29, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

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

- -

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.

Other links and lift over

dbSNP: rs71929101; hg19: chr10-76781905; API