rs1599961

Positions:

• chr4-102522412-G-A
• chr4-102522412-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003998.4(NFKB1):​c.-7-3100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,036 control chromosomes in the GnomAD database, including 12,548 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 0.40 (12548 hom., cov: 32)
• Consequence: NFKB1 NM_003998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFKB1	NM_003998.4	c.-7-3100G>A		intron_variant		ENST00000226574.9	NP_003989.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFKB1	ENST00000226574.9	c.-7-3100G>A		intron_variant		1	NM_003998.4	ENSP00000226574	P4

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61269 AN: 151920 Hom.: 12508 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.385

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.404 AC: 61363 AN: 152036 Hom.: 12548 Cov.: 32 AF XY: 0.406 AC XY: 30176 AN XY: 74328

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.381

Alfa AF: 0.386 Hom.: 19592

Bravo AF: 0.410

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.58
DANN	Benign	0.61

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

Other links and lift over

dbSNP: rs1599961; hg19: chr4-103443569;