rs201394549
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS1
The NM_001556.3(IKBKB):c.1126-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 1,579,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001556.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IKBKB | NM_001556.3 | c.1126-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000520810.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IKBKB | ENST00000520810.6 | c.1126-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001556.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251432Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135886
GnomAD4 exome AF: 0.000272 AC: 388AN: 1427308Hom.: 0 Cov.: 26 AF XY: 0.000246 AC XY: 175AN XY: 712524
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74292
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to IKK2 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at