19-13214601-G-T

Position:

• chr19-13214601-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The ENST00000360228.11(CACNA1A):​c.5739C>A​(p.Ala1913Ala) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A1913A) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1A ENST00000360228.11 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.58

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 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=-0.83).
• BP7: Synonymous conserved (PhyloP=-4.58 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.5739C>A	p.Ala1913Ala	synonymous_variant	39/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.5739C>A	p.Ala1913Ala	synonymous_variant	39/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.5757C>A	p.Ala1919Ala	synonymous_variant	40/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.5745C>A	p.Ala1915Ala	synonymous_variant	39/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.5601C>A	p.Ala1867Ala	synonymous_variant	38/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.5757C>A	p.Ala1919Ala	synonymous_variant	40/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.5748C>A	p.Ala1916Ala	synonymous_variant	40/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.5745C>A	p.Ala1915Ala	synonymous_variant	39/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.5742C>A	p.Ala1914Ala	synonymous_variant	39/46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.1	n.*41C>A		non_coding_transcript_exon_variant	4/10	5		ENSP00000490190.2
CACNA1A	ENST00000636768.1	n.*41C>A		3_prime_UTR_variant	4/10	5		ENSP00000490190.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs16044; hg19: chr19-13325415;