chr14-35401869-C-CAA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_020529.3(NFKBIA):c.*143_*144insTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 879,284 control chromosomes in the GnomAD database, including 378 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.023 ( 63 hom., cov: 32)
Exomes 𝑓: 0.025 ( 315 hom. )
Consequence
NFKBIA
NM_020529.3 3_prime_UTR
NM_020529.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.218
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 -10 ACMG points.
BP6
Variant 14-35401869-C-CAA is Benign according to our data. Variant chr14-35401869-C-CAA is described in ClinVar as [Likely_benign]. Clinvar id is 313104.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0563 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIA | NM_020529.3 | c.*143_*144insTT | 3_prime_UTR_variant | 6/6 | ENST00000216797.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIA | ENST00000216797.10 | c.*143_*144insTT | 3_prime_UTR_variant | 6/6 | 1 | NM_020529.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0229 AC: 3491AN: 152200Hom.: 62 Cov.: 32
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GnomAD4 exome AF: 0.0249 AC: 18066AN: 726966Hom.: 315 Cov.: 9 AF XY: 0.0256 AC XY: 9832AN XY: 384288
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GnomAD4 genome AF: 0.0230 AC: 3498AN: 152318Hom.: 63 Cov.: 32 AF XY: 0.0229 AC XY: 1703AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ectodermal dysplasia and immunodeficiency 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at