rs61751429
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001291415.2(KDM6A):c.1683+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,113,530 control chromosomes in the GnomAD database, including 7 homozygotes. There are 1,207 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0027 ( 1 hom., 78 hem., cov: 22)
Exomes 𝑓: 0.0040 ( 6 hom. 1129 hem. )
Consequence
KDM6A
NM_001291415.2 splice_donor_region, intron
NM_001291415.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0001326
2
Clinical Significance
Conservation
PhyloP100: 0.965
Genes affected
KDM6A (HGNC:12637): (lysine demethylase 6A) This gene is located on the X chromosome and is the corresponding locus to a Y-linked gene which encodes a tetratricopeptide repeat (TPR) protein. The encoded protein of this gene contains a JmjC-domain and catalyzes the demethylation of tri/dimethylated histone H3. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant X-45062751-G-A is Benign according to our data. Variant chrX-45062751-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 261406.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-45062751-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00274 (307/112215) while in subpopulation NFE AF= 0.00473 (252/53228). AF 95% confidence interval is 0.00425. There are 1 homozygotes in gnomad4. There are 78 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd at 78 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM6A | NM_001291415.2 | c.1683+3G>A | splice_donor_region_variant, intron_variant | ENST00000611820.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM6A | ENST00000611820.5 | c.1683+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_001291415.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00274 AC: 307AN: 112161Hom.: 1 Cov.: 22 AF XY: 0.00227 AC XY: 78AN XY: 34319
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GnomAD3 exomes AF: 0.00254 AC: 460AN: 181089Hom.: 0 AF XY: 0.00270 AC XY: 178AN XY: 65817
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GnomAD4 exome AF: 0.00399 AC: 3991AN: 1001315Hom.: 6 Cov.: 20 AF XY: 0.00392 AC XY: 1129AN XY: 288221
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GnomAD4 genome ? AF: 0.00274 AC: 307AN: 112215Hom.: 1 Cov.: 22 AF XY: 0.00227 AC XY: 78AN XY: 34383
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 24, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 18, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Kabuki syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 15, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at