10-18140981-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000282343.13(CACNB2):c.-199C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00041 in 1,518,994 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 3 hom. )
Consequence
CACNB2
ENST00000282343.13 5_prime_UTR
ENST00000282343.13 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.32
Genes affected
CACNB2 (HGNC:1402): (calcium voltage-gated channel auxiliary subunit beta 2) This gene encodes a subunit of a voltage-dependent calcium channel protein that is a member of the voltage-gated calcium channel superfamily. The gene product was originally identified as an antigen target in Lambert-Eaton myasthenic syndrome, an autoimmune disorder. Mutations in this gene are associated with Brugada syndrome. Alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Feb 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 10-18140981-C-T is Benign according to our data. Variant chr10-18140981-C-T is described in ClinVar as [Benign]. Clinvar id is 1292374.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 64 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNB2 | NM_201596.3 | c.120+125C>T | intron_variant | ENST00000324631.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNB2 | ENST00000324631.13 | c.120+125C>T | intron_variant | 1 | NM_201596.3 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 65AN: 152166Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000409 AC: 559AN: 1366710Hom.: 3 Cov.: 32 AF XY: 0.000379 AC XY: 254AN XY: 670838
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GnomAD4 genome AF: 0.000420 AC: 64AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at