rs2230018
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001291415.2(KDM6A):c.2333C>A(p.Thr778Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,208,646 control chromosomes in the GnomAD database, including 7,744 homozygotes. There are 51,061 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T778M) has been classified as Likely benign.
Frequency
Consequence
NM_001291415.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM6A | NM_001291415.2 | c.2333C>A | p.Thr778Lys | missense_variant | 18/30 | ENST00000611820.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM6A | ENST00000611820.5 | c.2333C>A | p.Thr778Lys | missense_variant | 18/30 | 1 | NM_001291415.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.102 AC: 11368AN: 111179Hom.: 595 Cov.: 22 AF XY: 0.0997 AC XY: 3326AN XY: 33367
GnomAD3 exomes AF: 0.134 AC: 24296AN: 181656Hom.: 1412 AF XY: 0.137 AC XY: 9117AN XY: 66342
GnomAD4 exome AF: 0.129 AC: 141123AN: 1097410Hom.: 7151 Cov.: 32 AF XY: 0.132 AC XY: 47735AN XY: 362846
GnomAD4 genome ? AF: 0.102 AC: 11367AN: 111236Hom.: 593 Cov.: 22 AF XY: 0.0995 AC XY: 3326AN XY: 33434
ClinVar
Submissions by phenotype
not specified Benign:3Other:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 29, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 01, 2013 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
Kabuki syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at