rs12409804

chr1-206483839-T-Achr1-206483839-T-C

Variant summary

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

The NM_014002.4(IKBKE):c.1428-1158T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,186 control chromosomes in the GnomAD database, including 5,318 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 0.25 (5318 hom., cov: 33)
• Consequence: IKBKE NM_014002.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

Genes affected

IKBKE (HGNC:14552): (inhibitor of nuclear factor kappa B kinase subunit epsilon) IKBKE is a noncanonical I-kappa-B (see MIM 164008) kinase (IKK) that is essential for regulating antiviral signaling pathways. IKBKE has also been identified as a breast cancer (MIM 114480) oncogene and is amplified and overexpressed in over 30% of breast carcinomas and breast cancer cell lines (Hutti et al., 2009 [PubMed 19481526]).[supplied by OMIM, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IKBKE	NM_014002.4	c.1428-1158T>A		intron_variant		ENST00000581977.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IKBKE	ENST00000581977.7	c.1428-1158T>A		intron_variant		1	NM_014002.4	P1
IKBKE	ENST00000578328.6	c.1428-1158T>A		intron_variant		1
IKBKE	ENST00000584998.5	c.1173-1158T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37718 AN: 152068 Hom.: 5321 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.248 AC: 37713 AN: 152186 Hom.: 5318 Cov.: 33 AF XY: 0.255 AC XY: 18988 AN XY: 74390

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.288

Alfa AF: 0.236 Hom.: 621

Bravo AF: 0.255

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.33

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: rs12409804; hg19: chr1-206657181;