rs704329

chr1-181758137-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001205293.3(CACNA1E):c.4494+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 1,603,568 control chromosomes in the GnomAD database, including 156,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (11469 hom., cov: 32)
  • Exomes 𝑓: 0.44 (145461 hom.)
• Consequence: CACNA1E NM_001205293.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.442

Genes affected

CACNA1E (HGNC:1392): (calcium voltage-gated channel subunit alpha1 E) Voltage-dependent calcium channels are multisubunit complexes consisting of alpha-1, alpha-2, beta, and delta subunits in a 1:1:1:1 ratio. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This gene encodes the alpha-1E subunit of the R-type calcium channels, which belong to the 'high-voltage activated' group that maybe involved in the modulation of firing patterns of neurons important for information processing. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-181758137-G-A is Benign according to our data. Variant chr1-181758137-G-A is described in ClinVar as [Benign]. Clinvar id is 1292555.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1E	NM_001205293.3	c.4494+26G>A		intron_variant		ENST00000367573.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1E	ENST00000367573.7	c.4494+26G>A		intron_variant		1	NM_001205293.3	A2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56239 AN: 151910 Hom.: 11455 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.352

GnomAD3 exomes AF: 0.408 AC: 99866 AN: 244522 Hom.: 21241 AF XY: 0.417 AC XY: 55272 AN XY: 132432

Gnomad AFR exome AF: 0.182

Gnomad AMR exome AF: 0.315

Gnomad ASJ exome AF: 0.412

Gnomad EAS exome AF: 0.399

Gnomad SAS exome AF: 0.415

Gnomad FIN exome AF: 0.464

Gnomad NFE exome AF: 0.458

Gnomad OTH exome AF: 0.401

GnomAD4 exome AF: 0.444 AC: 644319 AN: 1451540 Hom.: 145461 Cov.: 31 AF XY: 0.444 AC XY: 320164 AN XY: 721164

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.319

Gnomad4 ASJ exome AF: 0.415

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.415

Gnomad4 FIN exome AF: 0.462

Gnomad4 NFE exome AF: 0.461

Gnomad4 OTH exome AF: 0.414

GnomAD4 genome AF: 0.370 AC: 56277 AN: 152028 Hom.: 11469 Cov.: 32 AF XY: 0.372 AC XY: 27662 AN XY: 74314

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.357

Alfa AF: 0.433 Hom.: 20999

Bravo AF: 0.350

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.70
Dann	Benign	0.45

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: rs704329; hg19: chr1-181727273; COSMIC: COSV62392227;