chr7-82066526-TA-T
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000722.4(CACNA2D1):c.659-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 111,628 control chromosomes in the GnomAD database, including 240 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.047 ( 240 hom., cov: 27)
Exomes 𝑓: 0.31 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
CACNA2D1
NM_000722.4 splice_region, intron
NM_000722.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.04
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 Benign. Variant got -16 ACMG points.
BP6
Variant 7-82066526-TA-T is Benign according to our data. Variant chr7-82066526-TA-T is described in ClinVar as [Benign]. Clinvar id is 416576.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-82066526-TA-T is described in Lovd as [Benign]. Variant chr7-82066526-TA-T is described in Lovd as [Likely_benign]. Variant chr7-82066526-TA-T is described in Lovd as [Benign]. Variant chr7-82066526-TA-T is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0471 AC: 5259AN: 111650Hom.: 240 Cov.: 27
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GnomAD3 exomes AF: 0.337 AC: 30495AN: 90532Hom.: 1 AF XY: 0.340 AC XY: 16508AN XY: 48522
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.311 AC: 346937AN: 1116808Hom.: 2 Cov.: 0 AF XY: 0.310 AC XY: 171845AN XY: 553670
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GnomAD4 genome AF: 0.0472 AC: 5266AN: 111628Hom.: 240 Cov.: 27 AF XY: 0.0482 AC XY: 2551AN XY: 52924
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 02, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 16, 2019 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at