rs148656104
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020529.3(NFKBIA):āc.581G>Cā(p.Gly194Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000471 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G194D) has been classified as Uncertain significance.
Frequency
Consequence
NM_020529.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIA | NM_020529.3 | c.581G>C | p.Gly194Ala | missense_variant | 4/6 | ENST00000216797.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIA | ENST00000216797.10 | c.581G>C | p.Gly194Ala | missense_variant | 4/6 | 1 | NM_020529.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00264 AC: 401AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000669 AC: 168AN: 251126Hom.: 1 AF XY: 0.000486 AC XY: 66AN XY: 135758
GnomAD4 exome AF: 0.000246 AC: 360AN: 1461868Hom.: 1 Cov.: 36 AF XY: 0.000193 AC XY: 140AN XY: 727236
GnomAD4 genome AF: 0.00263 AC: 401AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.00265 AC XY: 197AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 24, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 23, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Ectodermal dysplasia and immunodeficiency 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
NFKBIA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | NFKBIA: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at