chr10-75022093-G-GGAGGAGGAAGAA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_012330.4(KAT6B):c.3252_3263dup(p.Glu1086_Glu1089dup) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.0000722 in 1,607,312 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00038 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000041 ( 0 hom. )
Consequence
KAT6B
NM_012330.4 inframe_insertion
NM_012330.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.76
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 -10 ACMG points.
BP6
?
Variant 10-75022093-G-GGAGGAGGAAGAA is Benign according to our data. Variant chr10-75022093-G-GGAGGAGGAAGAA is described in ClinVar as [Likely_benign]. Clinvar id is 1663325.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000376 (57/151502) while in subpopulation AFR AF= 0.00121 (50/41212). AF 95% confidence interval is 0.000945. There are 0 homozygotes in gnomad4. There are 31 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 57 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6B | NM_012330.4 | c.3252_3263dup | p.Glu1086_Glu1089dup | inframe_insertion | 16/18 | ENST00000287239.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6B | ENST00000287239.10 | c.3252_3263dup | p.Glu1086_Glu1089dup | inframe_insertion | 16/18 | 1 | NM_012330.4 | P2 | |
ENST00000413431.1 | n.65+3016_65+3017insTTCTTCCTCCTC | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000376 AC: 57AN: 151502Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000101 AC: 25AN: 247568Hom.: 0 AF XY: 0.0000820 AC XY: 11AN XY: 134134
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GnomAD4 exome AF: 0.0000405 AC: 59AN: 1455810Hom.: 0 Cov.: 33 AF XY: 0.0000400 AC XY: 29AN XY: 724312
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Genitopatellar syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at