19-38905388-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002503.5(NFKBIB):c.472C>T(p.Pro158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,613,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIB | NM_002503.5 | c.472C>T | p.Pro158Ser | missense_variant | 3/6 | ENST00000313582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIB | ENST00000313582.6 | c.472C>T | p.Pro158Ser | missense_variant | 3/6 | 1 | NM_002503.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 75AN: 247466Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 134738
GnomAD4 exome AF: 0.000183 AC: 268AN: 1461338Hom.: 0 Cov.: 32 AF XY: 0.000177 AC XY: 129AN XY: 726976
GnomAD4 genome AF: 0.000217 AC: 33AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.472C>T (p.P158S) 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 472, causing the proline (P) at amino acid position 158 to be replaced by a serine (S). 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