X-44873599-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001291421.2(KDM6A):c.-585C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,205,882 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001291421.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM6A | NM_001291415.2 | c.48C>T | p.Ala16Ala | synonymous_variant | 1/30 | ENST00000611820.5 | NP_001278344.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM6A | ENST00000611820.5 | c.48C>T | p.Ala16Ala | synonymous_variant | 1/30 | 1 | NM_001291415.2 | ENSP00000483595.2 |
Frequencies
GnomAD3 genomes AF: 0.00000887 AC: 1AN: 112688Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34842
GnomAD4 exome AF: 9.15e-7 AC: 1AN: 1093194Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 359840
GnomAD4 genome AF: 0.00000887 AC: 1AN: 112688Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34842
ClinVar
Submissions by phenotype
Kabuki syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at