10-75028886-AGAGGAGGAG-AGAG
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_012330.4(KAT6B):c.4074_4079delGGAGGA(p.Glu1359_Glu1360del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00165 in 1,609,654 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 4 hom. )
Consequence
KAT6B
NM_012330.4 disruptive_inframe_deletion
NM_012330.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.65
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant 10-75028886-AGAGGAG-A is Benign according to our data. Variant chr10-75028886-AGAGGAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 260241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-75028886-AGAGGAG-A is described in Lovd as [Likely_pathogenic]. Variant chr10-75028886-AGAGGAG-A is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd4 at 203 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00135 AC: 203AN: 150732Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00106 AC: 261AN: 245752Hom.: 0 AF XY: 0.00110 AC XY: 146AN XY: 133306
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GnomAD4 exome AF: 0.00168 AC: 2446AN: 1458804Hom.: 4 AF XY: 0.00157 AC XY: 1142AN XY: 725894
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GnomAD4 genome AF: 0.00135 AC: 203AN: 150850Hom.: 0 Cov.: 32 AF XY: 0.00118 AC XY: 87AN XY: 73772
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Genitopatellar syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | KAT6B: PS2:Moderate, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2017 | This variant is associated with the following publications: (PMID: 28857140, 26370006, 26334766, 25424711) - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Genitopatellar syndrome;C1863557:Blepharophimosis - intellectual disability syndrome, SBBYS type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 04, 2022 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at