10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAAGAA
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_012330.4(KAT6B):c.3307_3312dupGAAGAA(p.Glu1103_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 0.0000374 in 1,605,900 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 22)
Exomes 𝑓: 0.000040 ( 0 hom. )
Consequence
KAT6B
NM_012330.4 conservative_inframe_insertion
NM_012330.4 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.08
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 Likely_benign. Variant got -5 ACMG points.
BP6
Variant 10-75022147-G-GGAAGAA is Benign according to our data. Variant chr10-75022147-G-GGAAGAA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1388063.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
High AC in GnomAdExome4 at 58 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150036Hom.: 0 Cov.: 22
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GnomAD3 exomes AF: 0.0000126 AC: 3AN: 238206Hom.: 0 AF XY: 0.00000772 AC XY: 1AN XY: 129600
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GnomAD4 exome AF: 0.0000398 AC: 58AN: 1455864Hom.: 0 Cov.: 31 AF XY: 0.0000331 AC XY: 24AN XY: 724470
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GnomAD4 genome AF: 0.0000133 AC: 2AN: 150036Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 73172
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Genitopatellar syndrome;C1863557:Blepharophimosis - intellectual disability syndrome, SBBYS type Uncertain:1
Oct 24, 2021
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Genitopatellar syndrome Benign:1
Jul 12, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at