19-38908637-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001369699.1(NFKBIB):c.*930C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,442,270 control chromosomes in the GnomAD database, including 39,023 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 0.19 ( 3109 hom., cov: 30)
Exomes 𝑓: 0.23 ( 35914 hom. )
Consequence
NFKBIB
NM_001369699.1 3_prime_UTR
NM_001369699.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.930
Genes affected
NFKBIB (HGNC:7798): (NFKB inhibitor beta) The protein encoded by this gene belongs to the NF-kappa-B inhibitor family, which inhibit NF-kappa-B by complexing with, and trapping it in the cytoplasm. Phosphorylation of serine residues on these proteins by kinases marks them for destruction via the ubiquitination pathway, thereby allowing activation of the NF-kappa-B, which translocates to the nucleus to function as a transcription factor. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jul 2011]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFKBIB | NM_002503.5 | c.970-94C>T | intron_variant | ENST00000313582.6 | NP_002494.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFKBIB | ENST00000313582.6 | c.970-94C>T | intron_variant | 1 | NM_002503.5 | ENSP00000312988.5 | ||||
NFKBIB | ENST00000392079.7 | c.712-94C>T | intron_variant | 5 | ENSP00000375929.4 | |||||
NFKBIB | ENST00000509705.3 | n.*1693C>T | non_coding_transcript_exon_variant | 5/5 | 2 | ENSP00000438598.2 | ||||
NFKBIB | ENST00000509705.3 | n.*1693C>T | 3_prime_UTR_variant | 5/5 | 2 | ENSP00000438598.2 |
Frequencies
GnomAD3 genomes AF: 0.186 AC: 28083AN: 151390Hom.: 3110 Cov.: 30
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GnomAD4 exome AF: 0.232 AC: 299712AN: 1290774Hom.: 35914 Cov.: 35 AF XY: 0.235 AC XY: 147866AN XY: 629072
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GnomAD4 genome AF: 0.185 AC: 28084AN: 151496Hom.: 3109 Cov.: 30 AF XY: 0.184 AC XY: 13608AN XY: 74006
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ClinVar
Not reported inComputational scores
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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