17-7846859-T-TACCACCACCACC
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001348716.2(KDM6B):c.780_791dupACCACCACCACC(p.Pro261_Pro264dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,097,236 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001348716.2 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM6B | NM_001348716.2 | c.780_791dupACCACCACCACC | p.Pro261_Pro264dup | disruptive_inframe_insertion | Exon 10 of 24 | ENST00000448097.7 | NP_001335645.1 | |
KDM6B | NM_001080424.2 | c.780_791dupACCACCACCACC | p.Pro261_Pro264dup | disruptive_inframe_insertion | Exon 9 of 22 | NP_001073893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM6B | ENST00000448097.7 | c.780_791dupACCACCACCACC | p.Pro261_Pro264dup | disruptive_inframe_insertion | Exon 10 of 24 | 5 | NM_001348716.2 | ENSP00000412513.2 | ||
KDM6B | ENST00000254846.9 | c.780_791dupACCACCACCACC | p.Pro261_Pro264dup | disruptive_inframe_insertion | Exon 9 of 22 | 1 | ENSP00000254846.5 | |||
KDM6B | ENST00000570632.1 | c.711+147_711+158dupACCACCACCACC | intron_variant | Intron 7 of 8 | 5 | ENSP00000458445.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 271AN: 118286Hom.: 1 Cov.: 0 FAILED QC
GnomAD4 exome AF: 0.00188 AC: 2062AN: 1097236Hom.: 9 Cov.: 43 AF XY: 0.00182 AC XY: 1009AN XY: 554504
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00230 AC: 272AN: 118348Hom.: 1 Cov.: 0 AF XY: 0.00211 AC XY: 117AN XY: 55506
ClinVar
Submissions by phenotype
KDM6B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at