6-53036234-T-C

Position:

• chr6-53036234-T-C

Variant summary

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

The NM_014920.5(CILK1):​c.156+1705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,166 control chromosomes in the GnomAD database, including 2,795 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 0.18 (2795 hom., cov: 32)
• Consequence: CILK1 NM_014920.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CILK1	NM_014920.5	c.156+1705A>G		intron_variant		ENST00000676107.1	NP_055735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CILK1	ENST00000676107.1	c.156+1705A>G		intron_variant			NM_014920.5	ENSP00000501692.1
CILK1	ENST00000350082.10	c.156+1705A>G		intron_variant		1		ENSP00000263043.8
CILK1	ENST00000356971.3	c.156+1705A>G		intron_variant		2		ENSP00000349458.3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27806 AN: 152048 Hom.: 2781 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.183 AC: 27844 AN: 152166 Hom.: 2795 Cov.: 32 AF XY: 0.178 AC XY: 13211 AN XY: 74418

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.181

Alfa AF: 0.166 Hom.: 3739

Bravo AF: 0.190

Asia WGS AF: 0.0990 AC: 344 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.0
DANN	Benign	0.89

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: rs10484408; hg19: chr6-52901032;