rs1059704
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014002.4(IKBKE):c.358+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 1,607,262 control chromosomes in the GnomAD database, including 355,973 homozygotes. 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
Genomes: 𝑓 0.58 ( 27170 hom., cov: 31)
Exomes 𝑓: 0.67 ( 328803 hom. )
Consequence
IKBKE
NM_014002.4 intron
NM_014002.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.162
Genes affected
IKBKE (HGNC:14552): (inhibitor of nuclear factor kappa B kinase subunit epsilon) IKBKE is a noncanonical I-kappa-B (see MIM 164008) kinase (IKK) that is essential for regulating antiviral signaling pathways. IKBKE has also been identified as a breast cancer (MIM 114480) oncogene and is amplified and overexpressed in over 30% of breast carcinomas and breast cancer cell lines (Hutti et al., 2009 [PubMed 19481526]).[supplied by OMIM, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IKBKE | NM_014002.4 | c.358+41G>A | intron_variant | ENST00000581977.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IKBKE | ENST00000581977.7 | c.358+41G>A | intron_variant | 1 | NM_014002.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.583 AC: 88583AN: 151884Hom.: 27170 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.622 AC: 154526AN: 248360Hom.: 49527 AF XY: 0.630 AC XY: 84582AN XY: 134234
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GnomAD4 exome AF: 0.668 AC: 971506AN: 1455260Hom.: 328803 Cov.: 33 AF XY: 0.668 AC XY: 483112AN XY: 723376
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GnomAD4 genome ? AF: 0.583 AC: 88627AN: 152002Hom.: 27170 Cov.: 31 AF XY: 0.578 AC XY: 42965AN XY: 74284
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at