ENST00000394820.8:c.-449C>G

Variant names:

• chr4-102501347-C-G
• rs72696119
• ENST00000394820.8:c.-449C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000394820.8(NFKB1):​c.-449C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,462 control chromosomes in the GnomAD database, including 14,261 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (14245 hom., cov: 33)
  • Exomes 𝑓: 0.41 (16 hom.)
• Consequence: NFKB1 ENST00000394820.8 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 29 publications found

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]

NFKB1 Gene-Disease associations (from GenCC):

• immunodeficiency, common variable, 12

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
• common variable immunodeficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

NFKB1-AS1 (HGNC:58149):

ENSG00000260651 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000394820.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKB1-AS1	NR_136202.1		n.48+1092G>C		intron	N/A
	NFKB1	NM_003998.4	MANE Select	c.-449C>G		upstream_gene	N/A	NP_003989.2
	NFKB1	NM_001382626.1		c.-519C>G		upstream_gene	N/A	NP_001369555.1	P19838-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKB1	ENST00000394820.8	TSL:1	c.-449C>G		5_prime_UTR	Exon 1 of 24	ENSP00000378297.4	P19838-1
	NFKB1	ENST00000507079.6	TSL:5	c.-495C>G		5_prime_UTR	Exon 1 of 25	ENSP00000426147.2	D6RH30
	NFKB1	ENST00000938143.1		c.-449C>G		5_prime_UTR	Exon 1 of 24	ENSP00000608202.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 64883 AN: 151160 Hom.: 14219 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.412 AC: 80 AN: 194 Hom.: 16 Cov.: 0 AF XY: 0.392 AC XY: 51 AN XY: 130

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.333 AC: 6 AN: 18

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.364 AC: 8 AN: 22

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.433 AC: 58 AN: 134

Other (OTH) AF: 0.300 AC: 3 AN: 10

GnomAD4 genome AF: 0.429 AC: 64950 AN: 151268 Hom.: 14245 Cov.: 33 AF XY: 0.430 AC XY: 31805 AN XY: 73926

African (AFR) AF: 0.494 AC: 20468 AN: 41396

American (AMR) AF: 0.487 AC: 7409 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1152 AN: 3460

East Asian (EAS) AF: 0.405 AC: 2081 AN: 5144

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4603 AN: 10208

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26543 AN: 67710

Other (OTH) AF: 0.399 AC: 838 AN: 2102

Alfa AF: 0.289 Hom.: 727

Bravo AF: 0.439

Asia WGS AF: 0.345 AC: 1157 AN: 3358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.90
PhyloP100		0.95
PromoterAI		0.028	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs72696119;

hg19: chr4-103422504;