rs2482109

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_201596.3(CACNB2):​c.213+85266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,136 control chromosomes in the GnomAD database, including 55,756 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.85 ( 55756 hom., cov: 32)

Consequence

CACNB2
NM_201596.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.508
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNB2NM_201596.3 linkuse as main transcriptc.213+85266G>A intron_variant ENST00000324631.13 NP_963890.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNB2ENST00000324631.13 linkuse as main transcriptc.213+85266G>A intron_variant 1 NM_201596.3 ENSP00000320025 Q08289-1
ENST00000626127.2 linkuse as main transcriptn.27+24925C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.853
AC:
129705
AN:
152018
Hom.:
55700
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.940
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.864
Gnomad ASJ
AF:
0.738
Gnomad EAS
AF:
0.639
Gnomad SAS
AF:
0.744
Gnomad FIN
AF:
0.817
Gnomad MID
AF:
0.774
Gnomad NFE
AF:
0.836
Gnomad OTH
AF:
0.832
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.853
AC:
129821
AN:
152136
Hom.:
55756
Cov.:
32
AF XY:
0.851
AC XY:
63271
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.941
Gnomad4 AMR
AF:
0.865
Gnomad4 ASJ
AF:
0.738
Gnomad4 EAS
AF:
0.639
Gnomad4 SAS
AF:
0.743
Gnomad4 FIN
AF:
0.817
Gnomad4 NFE
AF:
0.836
Gnomad4 OTH
AF:
0.833
Alfa
AF:
0.845
Hom.:
9278
Bravo
AF:
0.861
Asia WGS
AF:
0.758
AC:
2635
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.12
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2482109; hg19: chr10-18525170; API