Genetic Variant NM_001278.5:c.2209-217_2209-208delAAAAAAAAAA (chr10-100189834-CTTTTTTTTTT-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

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

The NM_001278.5(CHUK):c.2209-217_2209-208delAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00018 in 139,134 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 0.00018 ( 0 hom., cov: 30)

Consequence

CHUK
NM_001278.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.586

Variant links:

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]

CHUK links:

ENSG00000236308 (HGNC:):

ENSG00000236308 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CHUK	NM_001278.5 link	c.2209-217_2209-208delAAAAAAAAAA	intron_variant	Intron 20 of 20	ENST00000370397.8	NP_001269.3	O15111
CHUK	NM_001320928.2 link	c.32-217_32-208delAAAAAAAAAA	intron_variant	Intron 20 of 20		NP_001307857.1
CHUK	XM_047424540.1 link	c.2208+1025_2208+1034delAAAAAAAAAA	intron_variant	Intron 20 of 20		XP_047280496.1
CHUK	XM_047424542.1 link	c.31+1025_31+1034delAAAAAAAAAA	intron_variant	Intron 20 of 20		XP_047280498.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CHUK	ENST00000370397.8 link	c.2209-217_2209-208delAAAAAAAAAA	intron_variant	Intron 20 of 20	1	NM_001278.5	ENSP00000359424.6	O15111
CHUK	ENST00000590930.5 link	n.3585-217_3585-208delAAAAAAAAAA	intron_variant	Intron 2 of 2	1
CHUK	ENST00000588656.1 link	n.240-217_240-208delAAAAAAAAAA	intron_variant	Intron 3 of 3	3
ENSG00000236308	ENST00000443919.1 link	n.-201_-192delTTTTTTTTTT	upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.000180

AC:

AN:

139120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00517

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.000180

AC:

AN:

139134

Hom.:

Cov.:

AF XY:

0.000298

AC XY:

AN XY:

67210

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00519

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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