Genetic Variant ENST00000356146.5:n.2308C>G (chr14-50342977-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000356146.5(CDKL1):n.2308C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000083 in 1,204,210 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 8.3e-7 ( 0 hom. )

Consequence

CDKL1
ENST00000356146.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Publications

0 publications found

Variant links:

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]

CDKL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKL1	NM_004196.7 link	c.364-755C>G		intron_variant	Intron 4 of 9	ENST00000395834.6	NP_004187.3	Q00532

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CDKL1	ENST00000356146.5 link	n.2308C>G	non_coding_transcript_exon_variant	Exon 16 of 20	1
CDKL1	ENST00000395834.6 link	c.364-755C>G	intron_variant	Intron 4 of 9	1	NM_004196.7	ENSP00000379176.2
CDKL1	ENST00000216378.2 link	c.367-755C>G	intron_variant	Intron 4 of 8	1		ENSP00000216378.2	Q00532-3A0A5H1ZRP5
CDKL1	ENST00000528197.5 link	n.422-755C>G	intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.30e-7

AC:

AN:

1204210

Hom.:

Cov.:

AF XY:

0.00000168

AC XY:

AN XY:

595710

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25956

American (AMR)

AF:

0.00

AC:

AN:

35936

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16574

East Asian (EAS)

AF:

0.00

AC:

AN:

16270

South Asian (SAS)

AF:

0.00

AC:

AN:

81210

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30844

Middle Eastern (MID)

AF:

0.000224

AC:

AN:

4464

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

949314

Other (OTH)

AF:

0.00

AC:

AN:

43642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.15

(source)

DANN

Benign

0.60

PhyloP100

-2.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over