chr19-38905364-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.448C>T(p.Arg150Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,430 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R150H) has been classified 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.448C>T | p.Arg150Cys | missense_variant | 3/6 | ENST00000313582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIB | ENST00000313582.6 | c.448C>T | p.Arg150Cys | missense_variant | 3/6 | 1 | NM_002503.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000330 AC: 8AN: 242670Hom.: 0 AF XY: 0.0000377 AC XY: 5AN XY: 132684
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1460128Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 726352
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.448C>T (p.R150C) alteration is located in exon 3 (coding exon 3) of the NFKBIB gene. This alteration results from a C to T substitution at nucleotide position 448, causing the arginine (R) at amino acid position 150 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