19-38907615-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002503.5(NFKBIB):c.925G>A(p.Gly309Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000348 in 1,611,138 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.925G>A | p.Gly309Ser | missense_variant | 5/6 | ENST00000313582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIB | ENST00000313582.6 | c.925G>A | p.Gly309Ser | missense_variant | 5/6 | 1 | NM_002503.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000510 AC: 12AN: 235344Hom.: 0 AF XY: 0.0000386 AC XY: 5AN XY: 129612
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1458778Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 725568
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.925G>A (p.G309S) alteration is located in exon 5 (coding exon 5) of the NFKBIB gene. This alteration results from a G to A substitution at nucleotide position 925, causing the glycine (G) at amino acid position 309 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