rs201681631

Positions:

• chr19-13231716-C-A
• chr19-13231716-C-T

Variant summary

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

The NM_001127222.2(CACNA1A):​c.5394G>T​(p.Ser1798Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,986 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.87

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_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=-0.49).
• BP7: Synonymous conserved (PhyloP=-5.87 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.5394G>T	p.Ser1798Ser	synonymous_variant	35/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.5394G>T	p.Ser1798Ser	synonymous_variant	35/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.5412G>T	p.Ser1804Ser	synonymous_variant	36/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.5400G>T	p.Ser1800Ser	synonymous_variant	35/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.5256G>T	p.Ser1752Ser	synonymous_variant	34/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.5412G>T	p.Ser1804Ser	synonymous_variant	36/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.5403G>T	p.Ser1801Ser	synonymous_variant	36/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.5400G>T	p.Ser1800Ser	synonymous_variant	35/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.5397G>T	p.Ser1799Ser	synonymous_variant	35/46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.1	n.21G>T		non_coding_transcript_exon_variant	1/10	5		ENSP00000490190.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1457986 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724946

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	0.013
DANN	Benign	0.58

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: rs201681631; hg19: chr19-13342530;