chr10-100189834-CT-C

Variant names:

• chr10-100189834-CT-C
• rs34571703
• NM_001278.5:c.2209-208delA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001278.5(CHUK):​c.2209-208delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000669 in 139,100 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00067 (0 hom., cov: 30)
• Consequence: CHUK NM_001278.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

CHUK (HGNC:1974): (component of inhibitor of nuclear factor kappa B kinase complex) This gene encodes a member of the serine/threonine protein kinase family. The encoded protein, a component of a cytokine-activated protein complex that is an inhibitor of the essential transcription factor NF-kappa-B complex, phosphorylates sites that trigger the degradation of the inhibitor via the ubiquination pathway, thereby activating the transcription factor. [provided by RefSeq, Jul 2008]

ENSG00000236308 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHUK	NM_001278.5	c.2209-208delA		intron_variant	Intron 20 of 20	ENST00000370397.8	NP_001269.3
CHUK	NM_001320928.2	c.*32-208delA		intron_variant	Intron 20 of 20		NP_001307857.1
CHUK	XM_047424540.1	c.2208+1034delA		intron_variant	Intron 20 of 20		XP_047280496.1
CHUK	XM_047424542.1	c.*31+1034delA		intron_variant	Intron 20 of 20		XP_047280498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHUK	ENST00000370397.8	c.2209-208delA		intron_variant	Intron 20 of 20	1	NM_001278.5	ENSP00000359424.6
CHUK	ENST00000590930.5	n.3585-208delA		intron_variant	Intron 2 of 2	1
CHUK	ENST00000588656.1	n.240-208delA		intron_variant	Intron 3 of 3	3
ENSG00000236308	ENST00000443919.1	n.-201delT		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.000669 AC: 93 AN: 139086 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000184

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000501

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00765

Gnomad SAS AF: 0.000904

Gnomad FIN AF: 0.00131

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000391

Gnomad OTH AF: 0.00159

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

GnomAD4 genome AF: 0.000669 AC: 93 AN: 139100 Hom.: 0 Cov.: 30 AF XY: 0.000833 AC XY: 56 AN XY: 67194

Gnomad4 AFR AF: 0.000184

Gnomad4 AMR AF: 0.000501

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00768

Gnomad4 SAS AF: 0.000909

Gnomad4 FIN AF: 0.00131

Gnomad4 NFE AF: 0.000391

Gnomad4 OTH AF: 0.00158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34571703; hg19: chr10-101949591;