Variant chr3-54879327-CTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_018398.3(CACNA2D3):c.1783-10_1783-9del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 1,330,808 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 0)

Exomes 𝑓: 0.029 ( 1 hom. )

Consequence

CACNA2D3
NM_018398.3 intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.06

Variant links:

Genes affected

CACNA2D3 (HGNC:15460): (calcium voltage-gated channel auxiliary subunit alpha2delta 3) This gene encodes a member of the alpha-2/delta subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Various versions of each of these subunits exist, either expressed from similar genes or the result of alternative splicing. Research on a highly similar protein in rabbit suggests the protein described in this record is cleaved into alpha-2 and delta subunits. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

CACNA2D3 links:

CACNA2D3-AS1 (HGNC:40702): (CACNA2D3 antisense RNA 1)

CACNA2D3-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 3-54879327-CTT-C is Benign according to our data. Variant chr3-54879327-CTT-C is described in ClinVar as [Benign]. Clinvar id is 3037580.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA2D3	NM_018398.3 linkuse as main transcript	c.1783-10_1783-9del		intron_variant		ENST00000474759.6
CACNA2D3-AS1	NR_046666.1 linkuse as main transcript	n.534-385_534-384del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA2D3	ENST00000474759.6 linkuse as main transcript	c.1783-10_1783-9del		intron_variant		1	NM_018398.3	P1	Q8IZS8-1
CACNA2D3-AS1	ENST00000471265.1 linkuse as main transcript	n.534-385_534-384del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00282

AC:

406

AN:

143804

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00666

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00200

Gnomad SAS

AF:

0.000884

Gnomad FIN

AF:

0.00236

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00333

Gnomad OTH

AF:

0.00557

GnomAD4 exome

AF:

0.0291

AC:

34515

AN:

1186966

Hom.:

AF XY:

0.0297

AC XY:

17653

AN XY:

593630

show subpopulations

Gnomad4 AFR exome

AF:

0.0184

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.0351

Gnomad4 EAS exome

AF:

0.135

Gnomad4 SAS exome

AF:

0.0460

Gnomad4 FIN exome

AF:

0.0407

Gnomad4 NFE exome

AF:

0.0218

Gnomad4 OTH exome

AF:

0.0281

GnomAD4 genome

AF:

0.00283

AC:

407

AN:

143842

Hom.:

Cov.:

AF XY:

0.00271

AC XY:

189

AN XY:

69680

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00659

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00220

Gnomad4 SAS

AF:

0.000889

Gnomad4 FIN

AF:

0.00236

Gnomad4 NFE

AF:

0.00334

Gnomad4 OTH

AF:

0.00553

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CACNA2D3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 29, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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