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 (★★).
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]
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.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Jul 27, 2015
Genetic Services Laboratory, University of Chicago
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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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
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Jun 08, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Sep 28, 2016
GeneDx
Significance: Benign
Review Status: flagged submission
Collection Method: clinical testing
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Genitopatellar syndrome Benign:1
Feb 04, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter