19-38908821-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002503.5(NFKBIB):c.1060C>T(p.Arg354Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 1,458,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002503.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIB | NM_002503.5 | c.1060C>T | p.Arg354Cys | missense_variant | 6/6 | ENST00000313582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIB | ENST00000313582.6 | c.1060C>T | p.Arg354Cys | missense_variant | 6/6 | 1 | NM_002503.5 | P1 | |
NFKBIB | ENST00000392079.7 | c.802C>T | p.Arg268Cys | missense_variant | 6/6 | 5 | |||
NFKBIB | ENST00000509705.3 | c.*1877C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247552Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134040
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458336Hom.: 0 Cov.: 34 AF XY: 0.00000827 AC XY: 6AN XY: 725684
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2024 | The c.1060C>T (p.R354C) alteration is located in exon 6 (coding exon 6) of the NFKBIB gene. This alteration results from a C to T substitution at nucleotide position 1060, causing the arginine (R) at amino acid position 354 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at