rs1265879

Variant names:

• chr14-50411265-A-G
• rs1265879
• ENST00000356146.5:n.37-617T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356146.5(CDKL1):​n.37-617T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 13 publications found

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]

ENSG00000258857 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKL1	ENST00000356146.5	n.37-617T>C		intron_variant	Intron 1 of 19	1
ENSG00000258857	ENST00000791132.1	n.470+3370A>G		intron_variant	Intron 4 of 4
ENSG00000258857	ENST00000791133.1	n.361+3370A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.429 AC: 17762 AN: 41440

American (AMR) AF: 0.821 AC: 12548 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4578 AN: 5150

South Asian (SAS) AF: 0.877 AC: 4220 AN: 4814

European-Finnish (FIN) AF: 0.831 AC: 8792 AN: 10586

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56862 AN: 67978

Other (OTH) AF: 0.750 AC: 1582 AN: 2108

Alfa AF: 0.804 Hom.: 174627

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
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1265879; hg19: chr14-50877983;