chrX-45064935-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001291415.2(KDM6A):c.2079+1118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 111,321 control chromosomes in the GnomAD database, including 1,717 homozygotes. There are 6,104 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001291415.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM6A | NM_001291415.2 | c.2079+1118A>G | intron_variant | ENST00000611820.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM6A | ENST00000611820.5 | c.2079+1118A>G | intron_variant | 1 | NM_001291415.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 20050AN: 111269Hom.: 1721 Cov.: 23 AF XY: 0.182 AC XY: 6097AN XY: 33437
GnomAD4 genome ? AF: 0.180 AC: 20041AN: 111321Hom.: 1717 Cov.: 23 AF XY: 0.182 AC XY: 6104AN XY: 33499
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at