rs149701177
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS1
The NM_001556.3(IKBKB):c.1669G>A(p.Gly557Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,599,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. G557G) has been classified as Likely benign.
Frequency
Consequence
NM_001556.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IKBKB | NM_001556.3 | c.1669G>A | p.Gly557Arg | missense_variant | 16/22 | ENST00000520810.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IKBKB | ENST00000520810.6 | c.1669G>A | p.Gly557Arg | missense_variant | 16/22 | 1 | NM_001556.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000935 AC: 22AN: 235370Hom.: 0 AF XY: 0.000102 AC XY: 13AN XY: 126834
GnomAD4 exome AF: 0.0000746 AC: 108AN: 1447576Hom.: 0 Cov.: 29 AF XY: 0.0000779 AC XY: 56AN XY: 719286
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74504
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to IKK2 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at