rs13278372

Variant summary

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

The NM_001556.3(IKBKB):​c.1987-1247A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,758 control chromosomes in the GnomAD database, including 43,349 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 0.71 ( 43157 hom., cov: 33)
Exomes 𝑓: 0.86 ( 192 hom. )

Consequence

IKBKB
NM_001556.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.159
Variant links:
Genes affected
IKBKB (HGNC:5960): (inhibitor of nuclear factor kappa B kinase subunit beta) The protein encoded by this gene phosphorylates the inhibitor in the inhibitor/NF-kappa-B complex, causing dissociation of the inhibitor and activation of NF-kappa-B. The encoded protein itself is found in a complex of proteins. Several transcript variants, some protein-coding and some not, have been found for this gene. [provided by RefSeq, Sep 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IKBKBNM_001556.3 linkuse as main transcriptc.1987-1247A>C intron_variant ENST00000520810.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IKBKBENST00000520810.6 linkuse as main transcriptc.1987-1247A>C intron_variant 1 NM_001556.3 P1O14920-1

Frequencies

GnomAD3 genomes
AF:
0.706
AC:
107377
AN:
152132
Hom.:
43147
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.938
Gnomad AMR
AF:
0.843
Gnomad ASJ
AF:
0.916
Gnomad EAS
AF:
0.853
Gnomad SAS
AF:
0.744
Gnomad FIN
AF:
0.810
Gnomad MID
AF:
0.832
Gnomad NFE
AF:
0.885
Gnomad OTH
AF:
0.763
GnomAD4 exome
AF:
0.856
AC:
435
AN:
508
Hom.:
192
Cov.:
0
AF XY:
0.853
AC XY:
331
AN XY:
388
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.958
Gnomad4 SAS exome
AF:
0.750
Gnomad4 FIN exome
AF:
0.625
Gnomad4 NFE exome
AF:
0.864
Gnomad4 OTH exome
AF:
0.833
GnomAD4 genome
AF:
0.705
AC:
107399
AN:
152250
Hom.:
43157
Cov.:
33
AF XY:
0.706
AC XY:
52578
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.284
Gnomad4 AMR
AF:
0.843
Gnomad4 ASJ
AF:
0.916
Gnomad4 EAS
AF:
0.852
Gnomad4 SAS
AF:
0.746
Gnomad4 FIN
AF:
0.810
Gnomad4 NFE
AF:
0.885
Gnomad4 OTH
AF:
0.762
Alfa
AF:
0.809
Hom.:
12812
Bravo
AF:
0.695
Asia WGS
AF:
0.703
AC:
2443
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
5.6
DANN
Benign
0.76

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: rs13278372; hg19: chr8-42182241; API