rs200092317
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001322934.2(NFKB2):c.1826G>A(p.Arg609Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000604 in 1,614,054 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001322934.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKB2 | NM_001322934.2 | c.1826G>A | p.Arg609Gln | missense_variant | 17/23 | ENST00000661543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKB2 | ENST00000661543.1 | c.1826G>A | p.Arg609Gln | missense_variant | 17/23 | NM_001322934.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.00140 AC: 213AN: 152146Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00108 AC: 269AN: 248910Hom.: 1 AF XY: 0.00119 AC XY: 161AN XY: 135150
GnomAD4 exome AF: 0.000521 AC: 762AN: 1461790Hom.: 3 Cov.: 39 AF XY: 0.000557 AC XY: 405AN XY: 727198
GnomAD4 genome ? AF: 0.00140 AC: 213AN: 152264Hom.: 1 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74452
ClinVar
Submissions by phenotype
Immunodeficiency, common variable, 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | NFKB2: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at