chr14-35401929-TTTC-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_020529.3(NFKBIA):c.*81_*83del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 1,522,486 control chromosomes in the GnomAD database, including 8,207 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.085 ( 930 hom., cov: 32)
Exomes 𝑓: 0.086 ( 7277 hom. )
Consequence
NFKBIA
NM_020529.3 3_prime_UTR
NM_020529.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.440
Genes affected
NFKBIA (HGNC:7797): (NFKB inhibitor alpha) This gene encodes a member of the NF-kappa-B inhibitor family, which contain multiple ankrin repeat domains. The encoded protein interacts with REL dimers to inhibit NF-kappa-B/REL complexes which are involved in inflammatory responses. The encoded protein moves between the cytoplasm and the nucleus via a nuclear localization signal and CRM1-mediated nuclear export. Mutations in this gene have been found in ectodermal dysplasia anhidrotic with T-cell immunodeficiency autosomal dominant disease. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 14-35401929-TTTC-T is Benign according to our data. Variant chr14-35401929-TTTC-T is described in ClinVar as [Benign]. Clinvar id is 313106.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIA | NM_020529.3 | c.*81_*83del | 3_prime_UTR_variant | 6/6 | ENST00000216797.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIA | ENST00000216797.10 | c.*81_*83del | 3_prime_UTR_variant | 6/6 | 1 | NM_020529.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0847 AC: 12881AN: 152082Hom.: 925 Cov.: 32
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GnomAD4 exome AF: 0.0856 AC: 117300AN: 1370286Hom.: 7277 AF XY: 0.0865 AC XY: 59375AN XY: 686264
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GnomAD4 genome ? AF: 0.0848 AC: 12900AN: 152200Hom.: 930 Cov.: 32 AF XY: 0.0902 AC XY: 6711AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 28% of patients studied by a panel of primary immunodeficiencies. Number of patients: 27. Only high quality variants are reported. - |
Ectodermal dysplasia and immunodeficiency 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2021 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at