Variant rs2053071 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002503.5(NFKBIB):c.179+80C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,409,268 control chromosomes in the GnomAD database, including 102,496 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 0.32 ( 9882 hom., cov: 32)

Exomes 𝑓: 0.38 ( 92614 hom. )

Consequence

NFKBIB
NM_002503.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.448

Variant links:

Genes affected

NFKBIB (HGNC:7798): (NFKB inhibitor beta) The protein encoded by this gene belongs to the NF-kappa-B inhibitor family, which inhibit NF-kappa-B by complexing with, and trapping it in the cytoplasm. Phosphorylation of serine residues on these proteins by kinases marks them for destruction via the ubiquitination pathway, thereby allowing activation of the NF-kappa-B, which translocates to the nucleus to function as a transcription factor. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jul 2011]

NFKBIB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFKBIB	NM_002503.5 linkuse as main transcript	c.179+80C>G		intron_variant		ENST00000313582.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFKBIB	ENST00000313582.6 linkuse as main transcript	c.179+80C>G		intron_variant		1	NM_002503.5	P1	Q15653-1

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49235

AN:

151996

Hom.:

9872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0895

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.341

GnomAD4 exome

AF:

0.378

AC:

475175

AN:

1257154

Hom.:

92614

AF XY:

0.381

AC XY:

233675

AN XY:

613682

show subpopulations

Gnomad4 AFR exome

AF:

0.0772

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.380

Gnomad4 EAS exome

AF:

0.591

Gnomad4 SAS exome

AF:

0.469

Gnomad4 FIN exome

AF:

0.439

Gnomad4 NFE exome

AF:

0.367

Gnomad4 OTH exome

AF:

0.383

GnomAD4 genome

AF:

0.324

AC:

49249

AN:

152114

Hom.:

9882

Cov.:

AF XY:

0.336

AC XY:

24965

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0892

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.387

Gnomad4 EAS

AF:

0.590

Gnomad4 SAS

AF:

0.486

Gnomad4 FIN

AF:

0.453

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.334

Hom.:

1337

Bravo

AF:

0.317

Asia WGS

AF:

0.555

AC:

1930

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.7

DANN

Benign

0.75

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over