1-181483501-CTTTTTTTTTTTT-CTTTTT

Variant names:

• chr1-181483501-CTTTTTTT-C
• rs111237511
• ENST00000367570:c.-236_-230delTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000367570(CACNA1E):​c.-236_-230delTTTTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000697 in 210,852 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00047 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0011 (0 hom.)
• Consequence: CACNA1E ENST00000367570 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 66 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1E	NM_001205293.3	c.-243_-237delTTTTTTT		upstream_gene_variant		ENST00000367573.7	NP_001192222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1E	ENST00000367570	c.-236_-230delTTTTTTT		5_prime_UTR_variant	Exon 1 of 47	1		ENSP00000356542.1
CACNA1E	ENST00000524607.6	c.435-235_435-229delTTTTTTT		intron_variant	Intron 2 of 11	5		ENSP00000432038.2
CACNA1E	ENST00000367573.7	c.-243_-237delTTTTTTT		upstream_gene_variant		1	NM_001205293.3	ENSP00000356545.2
CACNA1E	ENST00000360108.7	c.-243_-237delTTTTTTT		upstream_gene_variant		5		ENSP00000353222.3
CACNA1E	ENST00000621791.4	c.-243_-237delTTTTTTT		upstream_gene_variant		1		ENSP00000481619.1

Frequencies

GnomAD3 genomes AF: 0.000474 AC: 66 AN: 139214 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000299

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000846

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000776

Gnomad OTH AF: 0.000527

GnomAD4 exome AF: 0.00113 AC: 81 AN: 71606 Hom.: 0 AF XY: 0.00132 AC XY: 49 AN XY: 37240

Gnomad4 AFR exome AF: 0.00145

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000143

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00115

Gnomad4 NFE exome AF: 0.00139

Gnomad4 OTH exome AF: 0.00127

GnomAD4 genome AF: 0.000474 AC: 66 AN: 139246 Hom.: 0 Cov.: 29 AF XY: 0.000459 AC XY: 31 AN XY: 67472

Gnomad4 AFR AF: 0.000187

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000299

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000846

Gnomad4 NFE AF: 0.000776

Gnomad4 OTH AF: 0.000525

Bravo AF: 0.000370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs111237511; hg19: chr1-181452637;