NM_006030.4:c.2590-11_2590-10delCT

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_006030.4(CACNA2D2):c.2590-11_2590-10delCT variant causes a intron change. The variant allele was found at a frequency of 0.000258 in 1,613,830 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00025 ( 2 hom. )

Consequence

CACNA2D2
NM_006030.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.17

Publications

0 publications found

Variant links:

Genes affected

CACNA2D2 (HGNC:1400): (calcium voltage-gated channel auxiliary subunit alpha2delta 2) Calcium channels mediate the entry of calcium ions into the cell upon membrane polarization. This gene encodes the alpha-2/delta subunit of the voltage-dependent calcium channel complex. The complex consists of the main channel-forming subunit alpha-1, and auxiliary subunits alpha-2/delta, beta, and gamma. The auxiliary subunits function in the assembly and membrane localization of the complex, and modulate calcium currents and channel activation/inactivation kinetics. The subunit encoded by this gene undergoes post-translational cleavage to yield the extracellular alpha2 peptide and a membrane-anchored delta polypeptide. This subunit is a receptor for the antiepileptic drug, gabapentin. Mutations in this gene are associated with early infantile epileptic encephalopathy. Single nucleotide polymorphisms in this gene are correlated with increased sensitivity to opioid drugs. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

CACNA2D2 Gene-Disease associations (from GenCC):

cerebellar atrophy with seizures and variable developmental delay
Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
complex neurodevelopmental disorder
Inheritance: AR Classification: MODERATE Submitted by: ClinGen

CACNA2D2 links:

ENSG00000272104 (HGNC:):

ENSG00000272104 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 3-50366634-CAG-C is Benign according to our data. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-50366634-CAG-C is described in CliVar as Benign. Clinvar id is 416540.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA2D2	NM_006030.4 link	c.2590-11_2590-10delCT		intron_variant	Intron 29 of 37	ENST00000424201.7	NP_006021.2	Q9NY47-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CACNA2D2	ENST00000424201.7 link	c.2590-11_2590-10delCT	intron_variant	Intron 29 of 37	1	NM_006030.4	ENSP00000390329.2	Q9NY47-2
CACNA2D2	ENST00000423994.6 link	c.2611-8_2611-7delCT	splice_region_variant, intron_variant	Intron 30 of 38	5		ENSP00000407393.2	C9JVC9
CACNA2D2	ENST00000266039.7 link	c.2590-11_2590-10delCT	intron_variant	Intron 29 of 37	1		ENSP00000266039.3	Q9NY47-3
CACNA2D2	ENST00000360963.7 link	c.2383-11_2383-10delCT	intron_variant	Intron 29 of 37	1		ENSP00000354228.3	Q9NY47-4
ENSG00000272104	ENST00000606589.1 link	c.9+304_9+305delAG	intron_variant	Intron 3 of 3	3		ENSP00000476225.1	U3KQU4

Frequencies

GnomAD3 genomes

AF:

0.000342

AC:

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00386

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.000478

GnomAD2 exomes

AF:

0.000512

AC:

128

AN:

250098

AF XY:

0.000561

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00425

Gnomad NFE exome

AF:

0.000284

Gnomad OTH exome

AF:

0.000655

GnomAD4 exome

AF:

0.000250

AC:

365

AN:

1461526

Hom.:

AF XY:

0.000268

AC XY:

195

AN XY:

727024

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00416

AC:

221

AN:

53116

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000110

AC:

122

AN:

1111964

Other (OTH)

AF:

0.000364

AC:

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

AF:

0.000341

AC:

AN:

152304

Hom.:

Cov.:

AF XY:

0.000524

AC XY:

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0000241

AC:

AN:

41566

American (AMR)

AF:

0.00

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00386

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000132

AC:

AN:

68026

Other (OTH)

AF:

0.000473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.000378

Hom.:

Bravo

AF:

0.0000567

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy

Benign:1

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.2

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over