10-100189834-C-CT

Position:

• chr10-100189834-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001278.5(CHUK):​c.2209-208_2209-207insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 139,026 control chromosomes in the GnomAD database, including 848 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (848 hom., cov: 30)
• Consequence: CHUK NM_001278.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-100189834-C-CT is Benign according to our data. Variant chr10-100189834-C-CT is described in ClinVar as [Benign]. Clinvar id is 1223963.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHUK	NM_001278.5	c.2209-208_2209-207insA		intron_variant		ENST00000370397.8	NP_001269.3
CHUK	NM_001320928.2	c.*32-208_*32-207insA		intron_variant			NP_001307857.1
CHUK	XM_047424540.1	c.2208+1034_2208+1035insA		intron_variant			XP_047280496.1
CHUK	XM_047424542.1	c.*31+1034_*31+1035insA		intron_variant			XP_047280498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHUK	ENST00000370397.8	c.2209-208_2209-207insA		intron_variant		1	NM_001278.5	ENSP00000359424	P1
CHUK	ENST00000590930.5	n.3585-208_3585-207insA		intron_variant, non_coding_transcript_variant		1
CHUK	ENST00000588656.1	n.240-208_240-207insA		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 14436 AN: 139012 Hom.: 851 Cov.: 30

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0972

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.104 AC: 14441 AN: 139026 Hom.: 848 Cov.: 30 AF XY: 0.106 AC XY: 7145 AN XY: 67142

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0950

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.103

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

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;