chr10-18141037-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000282343.13(CACNB2):c.-143G>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 0.00262 in 1,543,294 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 50 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 41 hom. )
Consequence
CACNB2
ENST00000282343.13 5_prime_UTR
ENST00000282343.13 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.316
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 10-18141037-G-C is Benign according to our data. Variant chr10-18141037-G-C is described in ClinVar as [Benign]. Clinvar id is 1238565.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0133 (2031/152274) while in subpopulation AFR AF= 0.0458 (1905/41554). AF 95% confidence interval is 0.0441. There are 50 homozygotes in gnomad4. There are 961 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2021 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNB2 | NM_201596.3 | c.120+181G>C | intron_variant | ENST00000324631.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNB2 | ENST00000324631.13 | c.120+181G>C | intron_variant | 1 | NM_201596.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0133 AC: 2021AN: 152156Hom.: 49 Cov.: 32
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GnomAD4 exome AF: 0.00145 AC: 2015AN: 1391020Hom.: 41 Cov.: 32 AF XY: 0.00131 AC XY: 901AN XY: 685452
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GnomAD4 genome ? AF: 0.0133 AC: 2031AN: 152274Hom.: 50 Cov.: 32 AF XY: 0.0129 AC XY: 961AN XY: 74468
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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