chr3-54598520-T-A

Position:

• chr3-54598520-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018398.3(CACNA2D3):​c.963+16643T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,812 control chromosomes in the GnomAD database, including 6,653 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 0.28 (6653 hom., cov: 30)
• Consequence: CACNA2D3 NM_018398.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA2D3	NM_018398.3	c.963+16643T>A		intron_variant		ENST00000474759.6	NP_060868.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA2D3	ENST00000474759.6	c.963+16643T>A		intron_variant		1	NM_018398.3	ENSP00000419101	P1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42800 AN: 151694 Hom.: 6654 Cov.: 30

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.292

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.282 AC: 42800 AN: 151812 Hom.: 6653 Cov.: 30 AF XY: 0.276 AC XY: 20479 AN XY: 74182

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.289

Alfa AF: 0.323 Hom.: 1161

Bravo AF: 0.271

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs13064588; hg19: chr3-54632547;