chr19-13207403-G-A

Position:

chr19-13207403-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001127222.2(CACNA1A):c.7431C>T(p.Tyr2477=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00841 in 1,535,954 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0074 ( 11 hom., cov: 31)

Exomes 𝑓: 0.0085 ( 103 hom. )

Consequence

CACNA1A
NM_001127222.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.150

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 19-13207403-G-A is Benign according to our data. Variant chr19-13207403-G-A is described in ClinVar as [Benign]. Clinvar id is 257513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13207403-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.15 with no splicing effect.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00737 (1118/151678) while in subpopulation AMR AF= 0.0202 (308/15244). AF 95% confidence interval is 0.0183. There are 11 homozygotes in gnomad4. There are 580 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1118 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1A	NM_001127222.2 linkuse as main transcript	c.7431C>T	p.Tyr2477=	synonymous_variant	47/47	ENST00000360228.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1A	ENST00000360228.11 linkuse as main transcript	c.7431C>T	p.Tyr2477=	synonymous_variant	47/47	1	NM_001127222.2		O00555-8

Frequencies

GnomAD3 genomes

AF:

0.00734

AC:

1113

AN:

151570

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00182

Gnomad AMI

AF:

0.0399

Gnomad AMR

AF:

0.0201

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.00934

Gnomad SAS

AF:

0.00994

Gnomad FIN

AF:

0.00619

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00757

Gnomad OTH

AF:

0.00961

GnomAD3 exomes

AF:

0.0126

AC:

1749

AN:

139132

Hom.:

AF XY:

0.0116

AC XY:

892

AN XY:

77118

show subpopulations

Gnomad AFR exome

AF:

0.00133

Gnomad AMR exome

AF:

0.0327

Gnomad ASJ exome

AF:

0.000122

Gnomad EAS exome

AF:

0.0144

Gnomad SAS exome

AF:

0.0108

Gnomad FIN exome

AF:

0.00760

Gnomad NFE exome

AF:

0.00749

Gnomad OTH exome

AF:

0.0118

GnomAD4 exome

AF:

0.00852

AC:

11793

AN:

1384276

Hom.:

103

Cov.:

AF XY:

0.00864

AC XY:

5916

AN XY:

685000

show subpopulations

Gnomad4 AFR exome

AF:

0.00136

Gnomad4 AMR exome

AF:

0.0312

Gnomad4 ASJ exome

AF:

0.000323

Gnomad4 EAS exome

AF:

0.0101

Gnomad4 SAS exome

AF:

0.0104

Gnomad4 FIN exome

AF:

0.00853

Gnomad4 NFE exome

AF:

0.00801

Gnomad4 OTH exome

AF:

0.00805

GnomAD4 genome

AF:

0.00737

AC:

1118

AN:

151678

Hom.:

Cov.:

AF XY:

0.00782

AC XY:

580

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.00179

Gnomad4 AMR

AF:

0.0202

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.00937

Gnomad4 SAS

AF:

0.00974

Gnomad4 FIN

AF:

0.00619

Gnomad4 NFE

AF:

0.00757

Gnomad4 OTH

AF:

0.0119

Alfa

AF:

0.00448

Hom.:

Bravo

AF:

0.00870

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 14, 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	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Nov 04, 2019	- -

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

6.4

DANN

Benign

0.97

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over