rs782604431
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP5BP4BS2
The NM_001099857.5(IKBKG):c.185G>A(p.Arg62Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,185,714 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 46 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001099857.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IKBKG | NM_001099857.5 | c.185G>A | p.Arg62Gln | missense_variant, splice_region_variant | 2/10 | ENST00000594239.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IKBKG | ENST00000594239.6 | c.185G>A | p.Arg62Gln | missense_variant, splice_region_variant | 2/10 | 1 | NM_001099857.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000981 AC: 11AN: 112141Hom.: 0 Cov.: 23 AF XY: 0.0000875 AC XY: 3AN XY: 34283
GnomAD3 exomes AF: 0.0000241 AC: 4AN: 166227Hom.: 0 AF XY: 0.0000376 AC XY: 2AN XY: 53225
GnomAD4 exome AF: 0.000150 AC: 161AN: 1073573Hom.: 0 Cov.: 29 AF XY: 0.000125 AC XY: 43AN XY: 343741
GnomAD4 genome ? AF: 0.0000981 AC: 11AN: 112141Hom.: 0 Cov.: 23 AF XY: 0.0000875 AC XY: 3AN XY: 34283
ClinVar
Submissions by phenotype
Ectodermal dysplasia and immunodeficiency 1 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Department of Immunology, University Hospital Southampton NHSFT | - | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2021 | Unlikely to be causative of incontinentia pigmenti (XLD) Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | IKBKG: PS4:Supporting - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at