rs316144

Positions:

• chr6-53014897-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.832-915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,086 control chromosomes in the GnomAD database, including 28,777 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 0.58 (28777 hom., cov: 32)
• Consequence: CILK1 NM_014920.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CILK1	NM_014920.5	c.832-915G>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.832-915G>A		intron_variant			NM_014920.5	ENSP00000501692	P1
CILK1	ENST00000350082.10	c.832-915G>A		intron_variant		1		ENSP00000263043
CILK1	ENST00000356971.3	c.832-915G>A		intron_variant		2		ENSP00000349458	P1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87855 AN: 151968 Hom.: 28709 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.579 AC: 87985 AN: 152086 Hom.: 28777 Cov.: 32 AF XY: 0.570 AC XY: 42385 AN XY: 74338

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.549

Alfa AF: 0.473 Hom.: 23841

Bravo AF: 0.609

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.20

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: rs316144; hg19: chr6-52879695;