chr7-82066526-TAAA-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000722.4(CACNA2D1):c.659-5_659-3delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 1,430,140 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00074 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0027 ( 0 hom. )
Consequence
CACNA2D1
NM_000722.4 splice_region, intron
NM_000722.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.51
Genes affected
CACNA2D1 (HGNC:1399): (calcium voltage-gated channel auxiliary subunit alpha2delta 1) The preproprotein encoded by this gene is cleaved into multiple chains that comprise the alpha-2 and delta subunits of the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. Mutations in this gene can cause cardiac deficiencies, including Brugada syndrome and short QT syndrome. Alternate splicing results in multiple transcript variants, some of which may lack the delta subunit portion. [provided by RefSeq, Nov 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 7-82066526-TAAA-T is Benign according to our data. Variant chr7-82066526-TAAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317982.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 83 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000743 AC: 83AN: 111720Hom.: 0 Cov.: 27
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GnomAD3 exomes AF: 0.0128 AC: 1162AN: 90532Hom.: 0 AF XY: 0.0127 AC XY: 617AN XY: 48522
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GnomAD4 exome AF: 0.00265 AC: 3498AN: 1318420Hom.: 0 AF XY: 0.00270 AC XY: 1756AN XY: 650940
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GnomAD4 genome AF: 0.000743 AC: 83AN: 111720Hom.: 0 Cov.: 27 AF XY: 0.000680 AC XY: 36AN XY: 52948
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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
Aug 13, 2019
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at