chr8-42277660-A-C

Variant names:

• chr8-42277660-A-C
• rs11986055
• NM_001556.3:c.105+5455A>C

Variant summary

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

The NM_001556.3(IKBKB):​c.105+5455A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,762 control chromosomes in the GnomAD database, including 7,923 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 0.21 (7923 hom., cov: 31)
• Consequence: IKBKB NM_001556.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 18 publications found

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]

IKBKB Gene-Disease associations (from GenCC):

• severe combined immunodeficiency due to IKK2 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, Ambry Genetics
• immunodeficiency 15a

  Inheritance: AR, AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001556.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKB	NM_001556.3	MANE Select	c.105+5455A>C		intron	N/A	NP_001547.1
	IKBKB	NM_001242778.2		c.23+5455A>C		intron	N/A	NP_001229707.1
	IKBKB	NM_001190720.3		c.-88+6191A>C		intron	N/A	NP_001177649.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKB	ENST00000520810.6	TSL:1 MANE Select	c.105+5455A>C		intron	N/A	ENSP00000430684.1
	IKBKB	ENST00000519735.5	TSL:1	n.275+5455A>C		intron	N/A
	IKBKB	ENST00000523517.5	TSL:1	n.105+5455A>C		intron	N/A	ENSP00000430114.1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32165 AN: 151644 Hom.: 7891 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.212 AC: 32245 AN: 151762 Hom.: 7923 Cov.: 31 AF XY: 0.214 AC XY: 15835 AN XY: 74152

African (AFR) AF: 0.600 AC: 24800 AN: 41364

American (AMR) AF: 0.0972 AC: 1482 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3464

East Asian (EAS) AF: 0.147 AC: 758 AN: 5150

South Asian (SAS) AF: 0.206 AC: 990 AN: 4808

European-Finnish (FIN) AF: 0.117 AC: 1227 AN: 10510

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2465 AN: 67906

Other (OTH) AF: 0.175 AC: 370 AN: 2112

Alfa AF: 0.0883 Hom.: 7104

Bravo AF: 0.224

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.48
PhyloP100		-0.53
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs11986055; hg19: chr8-42135178;