19-13286525-G-T

Position:

• chr19-13286525-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BS1 BS2

The NM_001127222.2(CACNA1A):​c.3531C>A​(p.Pro1177Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,492,082 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 Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00066 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00021 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 synonymous
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:4
• Conservation: PhyloP100: 0.436

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 19-13286525-G-T is Benign according to our data. Variant chr19-13286525-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 283514.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=4}.
• BP7: Synonymous conserved (PhyloP=0.436 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000664 (101/152090) while in subpopulation AFR AF= 0.00214 (89/41494). AF 95% confidence interval is 0.00178. There are 0 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 101 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.3531C>A	p.Pro1177Pro	synonymous_variant	20/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.3531C>A	p.Pro1177Pro	synonymous_variant	20/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.3543C>A	p.Pro1181Pro	synonymous_variant	20/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.3537C>A	p.Pro1179Pro	synonymous_variant	20/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.3393C>A	p.Pro1131Pro	synonymous_variant	19/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.3543C>A	p.Pro1181Pro	synonymous_variant	20/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.3537C>A	p.Pro1179Pro	synonymous_variant	20/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.3534C>A	p.Pro1178Pro	synonymous_variant	20/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes AF: 0.000665 AC: 101 AN: 151972 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000244 AC: 42 AN: 172470 Hom.: 0 AF XY: 0.000186 AC XY: 17 AN XY: 91494

Gnomad AFR exome AF: 0.00172

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.000274

Gnomad EAS exome AF: 0.000805

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000601

Gnomad NFE exome AF: 0.0000479

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000208 AC: 279 AN: 1339992 Hom.: 0 Cov.: 24 AF XY: 0.000201 AC XY: 133 AN XY: 660114

Gnomad4 AFR exome AF: 0.00236

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000449

Gnomad4 EAS exome AF: 0.00450

Gnomad4 SAS exome AF: 0.0000574

Gnomad4 FIN exome AF: 0.0000201

Gnomad4 NFE exome AF: 0.0000106

Gnomad4 OTH exome AF: 0.000163

GnomAD4 genome AF: 0.000664 AC: 101 AN: 152090 Hom.: 0 Cov.: 30 AF XY: 0.000686 AC XY: 51 AN XY: 74330

Gnomad4 AFR AF: 0.00214

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00175

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000877 Hom.: 0

Bravo AF: 0.000975

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 27, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2019	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Athena Diagnostics

Nov 29, 2016

- -

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

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2024

- -

Inborn genetic diseases Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 23, 2019

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.3
DANN	Benign	0.69

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: rs184723350; hg19: chr19-13397339;