9-137878128-G-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000718.4(CACNA1B):c.195G>A(p.Lys65Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CACNA1B
NM_000718.4 synonymous
NM_000718.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.47
Genes affected
CACNA1B (HGNC:1389): (calcium voltage-gated channel subunit alpha1 B) The protein encoded by this gene is the pore-forming subunit of an N-type voltage-dependent calcium channel, which controls neurotransmitter release from neurons. The encoded protein forms a complex with alpha-2, beta, and delta subunits to form the high-voltage activated channel. This channel is sensitive to omega-conotoxin-GVIA and omega-agatoxin-IIIA but insensitive to dihydropyridines. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 9-137878128-G-A is Benign according to our data. Variant chr9-137878128-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3770698.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.47 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1B | NM_000718.4 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 47 | ENST00000371372.6 | NP_000709.1 | |
CACNA1B | NM_001243812.2 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 47 | NP_001230741.1 | ||
LOC100133077 | NR_121583.1 | n.2692-2448C>T | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372.6 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | ||
CACNA1B | ENST00000371357.5 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360408.1 | |||
CACNA1B | ENST00000371363.5 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | |||
CACNA1B | ENST00000277551.6 | c.195G>A | p.Lys65Lys | synonymous_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD3 exomes AF: 0.0000773 AC: 19AN: 245756Hom.: 0 AF XY: 0.0000973 AC XY: 13AN XY: 133590
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000169 AC: 2AN: 1182088Hom.: 0 Cov.: 32 AF XY: 0.00000349 AC XY: 2AN XY: 573738
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome Cov.: 34
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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
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
CACNA1B: BP4, BP7 -
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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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