rs1173445536

Positions:

• chr19-13259689-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_001127222.2(CACNA1A):​c.4263C>T​(p.Leu1421Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,459,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.178

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]

CACNA1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 19-13259689-G-A is Benign according to our data. Variant chr19-13259689-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 542844.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.178 with no splicing effect.
• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.4263C>T	p.Leu1421Leu	synonymous_variant	27/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.4263C>T	p.Leu1421Leu	synonymous_variant	27/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.4275C>T	p.Leu1425Leu	synonymous_variant	27/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.4269C>T	p.Leu1423Leu	synonymous_variant	27/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.4125C>T	p.Leu1375Leu	synonymous_variant	26/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.4275C>T	p.Leu1425Leu	synonymous_variant	27/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.4269C>T	p.Leu1423Leu	synonymous_variant	27/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.4266C>T	p.Leu1422Leu	synonymous_variant	27/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD3 exomes AF: 0.0000123 AC: 3 AN: 244860 Hom.: 0 AF XY: 0.00000754 AC XY: 1 AN XY: 132634

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000270

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1459196 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2 AN XY: 725534

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: 0.00000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 29

Alfa AF: 0.0000312 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 10, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	4.2
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs1173445536; hg19: chr19-13370503;