rs966015688

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003998.4(NFKB1):ā€‹c.47A>Gā€‹(p.His16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,447,366 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

NFKB1
NM_003998.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0190
Variant links:
Genes affected
NFKB1 (HGNC:7794): (nuclear factor kappa B subunit 1) This gene encodes a 105 kD protein which can undergo cotranslational processing by the 26S proteasome to produce a 50 kD protein. The 105 kD protein is a Rel protein-specific transcription inhibitor and the 50 kD protein is a DNA binding subunit of the NF-kappa-B (NFKB) protein complex. NFKB is a transcription regulator that is activated by various intra- and extra-cellular stimuli such as cytokines, oxidant-free radicals, ultraviolet irradiation, and bacterial or viral products. Activated NFKB translocates into the nucleus and stimulates the expression of genes involved in a wide variety of biological functions. Inappropriate activation of NFKB has been associated with a number of inflammatory diseases while persistent inhibition of NFKB leads to inappropriate immune cell development or delayed cell growth. NFKB is a critical regulator of the immediate-early response to viral infection. Alternative splicing results in multiple transcript variants encoding different isoforms, at least one of which is proteolytically processed. [provided by RefSeq, Aug 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.047943413).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NFKB1NM_003998.4 linkc.47A>G p.His16Arg missense_variant Exon 3 of 24 ENST00000226574.9 NP_003989.2 P19838-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NFKB1ENST00000226574.9 linkc.47A>G p.His16Arg missense_variant Exon 3 of 24 1 NM_003998.4 ENSP00000226574.4 P19838-2
NFKB1ENST00000505458.5 linkc.47A>G p.His16Arg missense_variant Exon 3 of 24 1 ENSP00000424790.1 P19838-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000410
AC:
1
AN:
244106
Hom.:
0
AF XY:
0.00000758
AC XY:
1
AN XY:
132002
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000337
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.91e-7
AC:
1
AN:
1447366
Hom.:
0
Cov.:
28
AF XY:
0.00000139
AC XY:
1
AN XY:
720454
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
7.6
DANN
Benign
0.97
DEOGEN2
Benign
0.18
.;T;.;.;T;T
Eigen
Benign
-0.96
Eigen_PC
Benign
-0.89
FATHMM_MKL
Benign
0.072
N
LIST_S2
Benign
0.69
T;.;T;T;T;T
M_CAP
Benign
0.0041
T
MetaRNN
Benign
0.048
T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
L;L;.;.;L;.
PrimateAI
Benign
0.44
T
PROVEAN
Benign
-0.71
N;N;N;N;N;N
REVEL
Benign
0.036
Sift
Benign
0.12
T;T;T;T;T;T
Sift4G
Benign
0.27
T;T;T;T;T;T
Polyphen
0.085
B;B;.;.;B;.
Vest4
0.26
MutPred
0.25
Loss of catalytic residue at D18 (P = 0.1104);Loss of catalytic residue at D18 (P = 0.1104);.;.;Loss of catalytic residue at D18 (P = 0.1104);Loss of catalytic residue at D18 (P = 0.1104);
MVP
0.41
MPC
1.3
ClinPred
0.045
T
GERP RS
0.47
Varity_R
0.066
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs966015688; hg19: chr4-103451000; API