chr1-181483507-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000367570.6(CACNA1E):c.-238T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00652 in 344,416 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 44 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 9 hom. )
Consequence
CACNA1E
ENST00000367570.6 5_prime_UTR
ENST00000367570.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.56
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 1-181483507-T-C is Benign according to our data. Variant chr1-181483507-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1300371.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1974/151380) while in subpopulation AFR AF= 0.0447 (1840/41146). AF 95% confidence interval is 0.043. There are 44 homozygotes in gnomad4. There are 907 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1970 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1E | NM_001205293.3 | upstream_gene_variant | ENST00000367573.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1E | ENST00000367570.6 | c.-238T>C | 5_prime_UTR_variant | 1/47 | 1 | P4 | |||
CACNA1E | ENST00000533229.1 | n.197T>C | non_coding_transcript_exon_variant | 1/7 | 1 | ||||
CACNA1E | ENST00000524607.6 | c.435-237T>C | intron_variant | 5 | |||||
CACNA1E | ENST00000367573.7 | upstream_gene_variant | 1 | NM_001205293.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0130 AC: 1970AN: 151264Hom.: 43 Cov.: 31
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GnomAD4 exome AF: 0.00141 AC: 272AN: 193036Hom.: 9 Cov.: 0 AF XY: 0.00116 AC XY: 114AN XY: 98264
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GnomAD4 genome ? AF: 0.0130 AC: 1974AN: 151380Hom.: 44 Cov.: 31 AF XY: 0.0123 AC XY: 907AN XY: 73996
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 30, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at