chr6-53031573-C-T

Position:

• chr6-53031573-C-T

Variant summary

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

The NM_014920.5(CILK1):​c.279-429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,048 control chromosomes in the GnomAD database, including 37,863 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 0.70 (37863 hom., cov: 32)
• Consequence: CILK1 NM_014920.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

Genes affected

CILK1 (HGNC:21219): (ciliogenesis associated kinase 1) Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. This gene encodes an intestinal serine/threonine kinase harboring a dual phosphorylation site found in mitogen-activating protein (MAP) kinases. The protein localizes to the intestinal crypt region and is thought to be important in intestinal epithelial cell proliferation and differentiation. Alternative splicing has been observed at this locus and two variants, encoding the same isoform, have been identified. [provided by RefSeq, Jul 2008]

CILK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CILK1	NM_014920.5	c.279-429G>A		intron_variant		ENST00000676107.1	NP_055735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CILK1	ENST00000676107.1	c.279-429G>A		intron_variant			NM_014920.5	ENSP00000501692.1
CILK1	ENST00000350082.10	c.279-429G>A		intron_variant		1		ENSP00000263043.8
CILK1	ENST00000356971.3	c.279-429G>A		intron_variant		2		ENSP00000349458.3

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106433 AN: 151930 Hom.: 37838 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.700 AC: 106484 AN: 152048 Hom.: 37863 Cov.: 32 AF XY: 0.706 AC XY: 52462 AN XY: 74326

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.708

Alfa AF: 0.730 Hom.: 19939

Bravo AF: 0.696

Asia WGS AF: 0.845 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.2
DANN	Benign	0.85

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: rs222455; hg19: chr6-52896371;