chr14-50411265-A-G

Position:

• chr14-50411265-A-G

Variant summary

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

The ENST00000356146.5(CDKL1):​n.37-617T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,038 control chromosomes in the GnomAD database, including 42,361 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 0.72 (42361 hom., cov: 30)
• Consequence: CDKL1 ENST00000356146.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

CDKL1 (HGNC:1781): (cyclin dependent kinase like 1) This gene product is a member of a large family of CDC2-related serine/threonine protein kinases that accumulates primarily in the nucleus. [provided by RefSeq, Nov 2018]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKL1	ENST00000356146.5	n.37-617T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109948 AN: 151920 Hom.: 42350 Cov.: 30

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.723 AC: 109990 AN: 152038 Hom.: 42361 Cov.: 30 AF XY: 0.728 AC XY: 54075 AN XY: 74308

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.750

Alfa AF: 0.824 Hom.: 80228

Bravo AF: 0.711

Asia WGS AF: 0.846 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1265879; hg19: chr14-50877983;