rs1555731992

Positions:

• chr19-13212742-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_001127222.2(CACNA1A):​c.5941-2A>G variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000000754 in 1,325,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.5e-7 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 4.63

Genes affected

CACNA1A (HGNC:1388): (calcium voltage-gated channel subunit alpha1 A) Voltage-dependent calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas, the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1A subunit, which is predominantly expressed in neuronal tissue. Mutations in this gene are associated with 2 neurologic disorders, familial hemiplegic migraine and episodic ataxia 2. This gene also exhibits polymorphic variation due to (CAG)n-repeats. Multiple transcript variants encoding different isoforms have been found for this gene. In one set of transcript variants, the (CAG)n-repeats occur in the 3' UTR, and are not associated with any disease. But in another set of variants, an insertion extends the coding region to include the (CAG)n-repeats which encode a polyglutamine tract. Expansion of the (CAG)n-repeats from the normal 4-18 to 21-33 in the coding region is associated with spinocerebellar ataxia 6. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.014492754 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.7, offset of 24, new splice context is: ggacacccctcatgttccAGcgc. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-13212742-T-C is Pathogenic according to our data. Variant chr19-13212742-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 522037.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.5941-2A>G		splice_acceptor_variant, intron_variant		ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.5941-2A>G		splice_acceptor_variant, intron_variant		1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.5959-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.5947-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.5803-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.5959-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.5950-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.5947-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.5944-2A>G		splice_acceptor_variant, intron_variant		1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.5944-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000489777.1
CACNA1A	ENST00000636768.1	n.*243-2A>G		splice_acceptor_variant, intron_variant		5		ENSP00000490190.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.54e-7 AC: 1 AN: 1325966 Hom.: 0 Cov.: 30 AF XY: 0.00000155 AC XY: 1 AN XY: 647196

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.62e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 16, 2023

The c.5944-2A>G intronic variant results from an A to G substitution two nucleotides before coding exon 41 of the CACNA1A gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown._x000D_ _x000D_ _x000D_ _x000D_ ; however, it is unlikely to be causative of CACNA1A-related spinocerebellar ataxia. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.20
CADD	Pathogenic	34
DANN	Uncertain	0.98
Eigen	Pathogenic	0.88
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Pathogenic	0.98	D
GERP RS		4.5

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.71		Position offset: -26
DS_AL_spliceai		0.99		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555731992; hg19: chr19-13323556;