chr19-13298896-G-A

Position:

• chr19-13298896-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2 BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001127222.2(CACNA1A):​c.2737C>T​(p.Pro913Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,594,678 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P913P) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0062 (7 hom., cov: 32)
  • Exomes 𝑓: 0.00061 (10 hom.)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9
• Conservation: PhyloP100: 1.98

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 Benign. Variant got -19 ACMG points.

• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1A. . Gene score misZ 5.7845 (greater than the threshold 3.09). Trascript score misZ 3.9354 (greater than threshold 3.09). GenCC has associacion of gene with benign paroxysmal torticollis of infancy, developmental and epileptic encephalopathy, 42, undetermined early-onset epileptic encephalopathy, episodic ataxia type 2, familial or sporadic hemiplegic migraine, spinocerebellar ataxia type 6, Lennox-Gastaut syndrome, migraine, familial hemiplegic, 1.
• BP4: Computational evidence support a benign effect (MetaRNN=0.0057442784).
• BP6: Variant 19-13298896-G-A is Benign according to our data. Variant chr19-13298896-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 128548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13298896-G-A is described in Lovd as [Benign].
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00624 (951/152334) while in subpopulation AFR AF= 0.0216 (899/41576). AF 95% confidence interval is 0.0204. There are 7 homozygotes in gnomad4. There are 435 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 951 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.2737C>T	p.Pro913Ser	missense_variant	19/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.2737C>T	p.Pro913Ser	missense_variant	19/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.2749C>T	p.Pro917Ser	missense_variant	19/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.2743C>T	p.Pro915Ser	missense_variant	19/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.2740C>T	p.Pro914Ser	missense_variant	19/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.2740C>T	p.Pro914Ser	missense_variant	19/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.2740C>T	p.Pro914Ser	missense_variant	19/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.2599C>T	p.Pro867Ser	missense_variant	18/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.2740C>T	p.Pro914Ser	missense_variant	19/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.2749C>T	p.Pro917Ser	missense_variant	19/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.2740C>T	p.Pro914Ser	missense_variant	19/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.2743C>T	p.Pro915Ser	missense_variant	19/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.2740C>T	p.Pro914Ser	missense_variant	19/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.2740C>T	p.Pro914Ser	missense_variant	19/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.2740C>T	p.Pro914Ser	missense_variant	19/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes AF: 0.00621 AC: 946 AN: 152226 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00229

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00140 AC: 307 AN: 218646 Hom.: 5 AF XY: 0.000985 AC XY: 120 AN XY: 121888

Gnomad AFR exome AF: 0.0211

Gnomad AMR exome AF: 0.000771

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000581

Gnomad SAS exome AF: 0.0000675

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000303

Gnomad OTH exome AF: 0.000722

GnomAD4 exome AF: 0.000613 AC: 884 AN: 1442344 Hom.: 10 Cov.: 32 AF XY: 0.000517 AC XY: 371 AN XY: 717848

Gnomad4 AFR exome AF: 0.0215

Gnomad4 AMR exome AF: 0.000834

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000584

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000324

Gnomad4 OTH exome AF: 0.00145

GnomAD4 genome AF: 0.00624 AC: 951 AN: 152334 Hom.: 7 Cov.: 32 AF XY: 0.00584 AC XY: 435 AN XY: 74488

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.00229

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000735

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.000305 Hom.: 1

Bravo AF: 0.00677

ESP6500AA AF: 0.0182 AC: 65

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.00161 AC: 189

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 05, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Apr 24, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 12, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 26, 2020	- -

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	May 03, 2017	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Inborn genetic diseases Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 27, 2016

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. -

CACNA1A-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 14, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.76
DEOGEN2	Benign	0.026	.;.;T;.;.;.;.;.;.;T;.;.;.;T;.
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.022	N
LIST_S2	Uncertain	0.87	D;D;D;D;D;D;D;D;.;D;D;D;D;D;D
MetaRNN	Benign	0.0057	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.22	T
MutationAssessor	Benign	0.34	.;.;.;.;N;.;.;.;.;.;.;.;N;.;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-1.1	.;N;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Benign	0.27
Sift	Benign	0.073	.;T;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Benign	0.90	T;T;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.049
MVP		0.70
MPC		1.1
ClinPred		0.0042	T
GERP RS		3.2
Varity_R		0.11
gMVP		0.49

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: rs16020; hg19: chr19-13409710;