rs367889547
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001322934.2(NFKB2):c.2350G>A(p.Gly784Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,742 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001322934.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKB2 | NM_001322934.2 | c.2350G>A | p.Gly784Arg | missense_variant | 21/23 | ENST00000661543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKB2 | ENST00000661543.1 | c.2350G>A | p.Gly784Arg | missense_variant | 21/23 | NM_001322934.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248550Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 134866
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461412Hom.: 0 Cov.: 34 AF XY: 0.0000399 AC XY: 29AN XY: 726998
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74494
ClinVar
Submissions by phenotype
Immunodeficiency, common variable, 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at