3-54766289-T-C

Variant names:

• chr3-54766289-T-C
• rs1820616
• NM_018398.3:c.1380+1938T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018398.3(CACNA2D3):​c.1380+1938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,218 control chromosomes in the GnomAD database, including 65,763 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 0.93 (65763 hom., cov: 31)
• Consequence: CACNA2D3 NM_018398.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018398.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA2D3	NM_018398.3	MANE Select	c.1380+1938T>C		intron	N/A	NP_060868.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA2D3	ENST00000474759.6	TSL:1 MANE Select	c.1380+1938T>C		intron	N/A	ENSP00000419101.1
	CACNA2D3	ENST00000490478.5	TSL:1	c.1098+1938T>C		intron	N/A	ENSP00000417279.1
	CACNA2D3	ENST00000468658.1	TSL:1	n.*794+1938T>C		intron	N/A	ENSP00000417455.1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141074 AN: 152100 Hom.: 65706 Cov.: 31

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.928 AC: 141192 AN: 152218 Hom.: 65763 Cov.: 31 AF XY: 0.924 AC XY: 68784 AN XY: 74412

African (AFR) AF: 0.943 AC: 39161 AN: 41542

American (AMR) AF: 0.937 AC: 14328 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3312 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3136 AN: 5148

South Asian (SAS) AF: 0.867 AC: 4185 AN: 4826

European-Finnish (FIN) AF: 0.932 AC: 9876 AN: 10602

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64129 AN: 68010

Other (OTH) AF: 0.916 AC: 1937 AN: 2114

Alfa AF: 0.939 Hom.: 8145

Bravo AF: 0.927

Asia WGS AF: 0.771 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1820616; hg19: chr3-54800316;