rs3845430

chr1-181429384-G-A

Variant summary

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

The XR_001738319.2(LOC107985232):n.3696-1833G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,938 control chromosomes in the GnomAD database, including 12,352 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 0.40 (12352 hom., cov: 31)
• Consequence: LOC107985232 XR_001738319.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

Genes affected

LOC107985232 (HGNC:):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985232	XR_001738319.2	n.3696-1833G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1E	ENST00000524607.6	c.434+15804G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60506 AN: 151820 Hom.: 12342 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.399 AC: 60552 AN: 151938 Hom.: 12352 Cov.: 31 AF XY: 0.393 AC XY: 29161 AN XY: 74272

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.397

Alfa AF: 0.405 Hom.: 1575

Bravo AF: 0.402

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3845430; hg19: chr1-181398520;