10-102401275-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001322934.2(NFKB2):c.2167G>A(p.Asp723Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000632 in 1,611,764 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001322934.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000436 AC: 108AN: 247504Hom.: 0 AF XY: 0.000417 AC XY: 56AN XY: 134234
GnomAD4 exome AF: 0.000647 AC: 945AN: 1459626Hom.: 2 Cov.: 36 AF XY: 0.000602 AC XY: 437AN XY: 725944
GnomAD4 genome AF: 0.000480 AC: 73AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74312
ClinVar
Submissions by phenotype
NFKB2-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 08, 2024 | The NFKB2 c.2167G>A variant is predicted to result in the amino acid substitution p.Asp723Asn. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.097% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Immunodeficiency, common variable, 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at