rs610100

chr1-181809194-C-A

Variant summary

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

The ENST00000661326.1(ENSG00000288574):n.1772G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,062 control chromosomes in the GnomAD database, including 25,690 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 0.57 (25690 hom., cov: 32)
• Consequence: ENST00000661326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

(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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661326.1	n.1772G>T		non_coding_transcript_exon_variant	2/2
CACNA1E	ENST00000700190.1	c.499-3124C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87022 AN: 151944 Hom.: 25661 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.573 AC: 87096 AN: 152062 Hom.: 25690 Cov.: 32 AF XY: 0.568 AC XY: 42212 AN XY: 74336

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.597

Alfa AF: 0.634 Hom.: 20498

Bravo AF: 0.557

Asia WGS AF: 0.473 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.71
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs610100; hg19: chr1-181778329;