chr17-7846859-T-TACCACC
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong
The NM_001348716.2(KDM6B):c.786_791dup(p.Pro263_Pro264dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.76 ( 34367 hom., cov: 0)
Exomes 𝑓: 0.56 ( 124679 hom. )
Failed GnomAD Quality Control
Consequence
KDM6B
NM_001348716.2 inframe_insertion
NM_001348716.2 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.250
Genes affected
KDM6B (HGNC:29012): (lysine demethylase 6B) The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP6
Variant 17-7846859-T-TACCACC is Benign according to our data. Variant chr17-7846859-T-TACCACC is described in ClinVar as [Likely_benign]. Clinvar id is 254122.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM6B | NM_001348716.2 | c.786_791dup | p.Pro263_Pro264dup | inframe_insertion | 10/24 | ENST00000448097.7 | |
KDM6B | NM_001080424.2 | c.786_791dup | p.Pro263_Pro264dup | inframe_insertion | 9/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM6B | ENST00000448097.7 | c.786_791dup | p.Pro263_Pro264dup | inframe_insertion | 10/24 | 5 | NM_001348716.2 | A2 | |
KDM6B | ENST00000254846.9 | c.786_791dup | p.Pro263_Pro264dup | inframe_insertion | 9/22 | 1 | P2 | ||
KDM6B | ENST00000570632.1 | c.711+153_711+158dup | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 89411AN: 117718Hom.: 34351 Cov.: 0 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.565 AC: 614608AN: 1088244Hom.: 124679 Cov.: 43 AF XY: 0.559 AC XY: 307306AN XY: 549990
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.760 AC: 89456AN: 117782Hom.: 34367 Cov.: 0 AF XY: 0.750 AC XY: 41431AN XY: 55212
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 18, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | May 04, 2023 | European Non-Finnish population allele frequency is 77.92% (rs779500270, 8811/11110 alleles, 3564 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.4.0, this variant is classified as BENIGN. Following criteria are met: BA1 - |
Oromandibular-limb hypogenesis spectrum Uncertain:1
Uncertain significance, no assertion criteria provided | research | CHU Sainte-Justine Research Center, University of Montreal | Aug 12, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2021 | This variant is associated with the following publications: (PMID: 33337535) - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at