Variant 7-151055521-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004935.4(CDK5):c.483+11A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,611,246 control chromosomes in the GnomAD database, including 50,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5223 hom., cov: 33)

Exomes 𝑓: 0.24 ( 45773 hom. )

Consequence

CDK5
NM_004935.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.313

Variant links:

Genes affected

CDK5 (HGNC:1774): (cyclin dependent kinase 5) This gene encodes a proline-directed serine/threonine kinase that is a member of the cyclin-dependent kinase family of proteins. Unlike other members of the family, the protein encoded by this gene does not directly control cell cycle regulation. Instead the protein, which is predominantly expressed at high levels in mammalian postmitotic central nervous system neurons, functions in diverse processes such as synaptic plasticity and neuronal migration through phosphorylation of proteins required for cytoskeletal organization, endocytosis and exocytosis, and apoptosis. In humans, an allelic variant of the gene that results in undetectable levels of the protein has been associated with lethal autosomal recessive lissencephaly-7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]

CDK5 links:

CDK5 (HGNC:):

CDK5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 7-151055521-T-G is Benign according to our data. Variant chr7-151055521-T-G is described in ClinVar as [Benign]. Clinvar id is 1600506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK5	NM_004935.4 linkuse as main transcript	c.483+11A>C		intron_variant		ENST00000485972.6	NP_004926.1	Q00535-1A0A090N7W4
CDK5	NM_001164410.3 linkuse as main transcript	c.387+11A>C		intron_variant			NP_001157882.1	Q00535-2A0A0S2Z355

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CDK5	ENST00000485972.6 linkuse as main transcript	c.483+11A>C	intron_variant		1	NM_004935.4	ENSP00000419782.1	Q00535-1
CDK5	ENST00000297518.4 linkuse as main transcript	c.387+11A>C	intron_variant		1		ENSP00000297518.4	Q00535-2
CDK5	ENST00000476691.1 linkuse as main transcript	n.694A>C	non_coding_transcript_exon_variant	2/2	4
CDK5	ENST00000487703.5 linkuse as main transcript	n.847+11A>C	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38732

AN:

152054

Hom.:

5214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.288

AC:

71558

AN:

248186

Hom.:

12321

AF XY:

0.272

AC XY:

36655

AN XY:

134754

show subpopulations

Gnomad AFR exome

AF:

0.232

Gnomad AMR exome

AF:

0.574

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.330

Gnomad SAS exome

AF:

0.189

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.239

Gnomad OTH exome

AF:

0.278

GnomAD4 exome

AF:

0.241

AC:

351962

AN:

1459074

Hom.:

45773

Cov.:

AF XY:

0.239

AC XY:

173161

AN XY:

725948

show subpopulations

Gnomad4 AFR exome

AF:

0.232

Gnomad4 AMR exome

AF:

0.559

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.270

Gnomad4 NFE exome

AF:

0.229

Gnomad4 OTH exome

AF:

0.239

GnomAD4 genome

AF:

0.255

AC:

38755

AN:

152172

Hom.:

5223

Cov.:

AF XY:

0.258

AC XY:

19198

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.399

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.258

Alfa

AF:

0.241

Hom.:

5019

Bravo

AF:

0.272

Asia WGS

AF:

0.251

AC:

873

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.1

DANN

Benign

0.37

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over