NM_000719.7:c.3387G>A

Variant names:

• chr12-2608541-G-A
• rs188224114
• NM_000719.7:c.3387G>A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_000719.7(CACNA1C):​c.3387G>A​(p.Thr1129Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,612,720 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0048 (8 hom., cov: 32)
  • Exomes 𝑓: 0.00075 (9 hom.)
• Consequence: CACNA1C NM_000719.7 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: -0.806

Genes affected

CACNA1C (HGNC:1390): (calcium voltage-gated channel subunit alpha1 C) This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. The alpha-1 subunit consists of 24 transmembrane segments and forms the pore through which ions pass into the cell. The calcium channel consists of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. The protein encoded by this gene binds to and is inhibited by dihydropyridine. Alternative splicing results in many transcript variants encoding different proteins. Some of the predicted proteins may not produce functional ion channel subunits. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 12-2608541-G-A is Benign according to our data. Variant chr12-2608541-G-A is described in ClinVar as [Benign]. Clinvar id is 78960.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-2608541-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-0.806 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00476 (725/152270) while in subpopulation AFR AF= 0.0159 (660/41552). AF 95% confidence interval is 0.0149. There are 8 homozygotes in gnomad4. There are 327 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 725 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3537G>A	p.Thr1179Thr	synonymous_variant	Exon 28 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3552G>A	p.Thr1184Thr	synonymous_variant	Exon 28 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3447G>A	p.Thr1149Thr	synonymous_variant	Exon 28 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3477G>A	p.Thr1159Thr	synonymous_variant	Exon 27 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3477G>A	p.Thr1159Thr	synonymous_variant	Exon 27 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3477G>A	p.Thr1159Thr	synonymous_variant	Exon 27 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3477G>A	p.Thr1159Thr	synonymous_variant	Exon 27 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3462G>A	p.Thr1154Thr	synonymous_variant	Exon 28 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3447G>A	p.Thr1149Thr	synonymous_variant	Exon 28 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3462G>A	p.Thr1154Thr	synonymous_variant	Exon 28 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3378G>A	p.Thr1126Thr	synonymous_variant	Exon 27 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3387G>A	p.Thr1129Thr	synonymous_variant	Exon 27 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1994G>A		non_coding_transcript_exon_variant	Exon 25 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1994G>A		3_prime_UTR_variant	Exon 25 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes AF: 0.00475 AC: 723 AN: 152152 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.00383

GnomAD3 exomes AF: 0.00166 AC: 413 AN: 248434 Hom.: 4 AF XY: 0.00129 AC XY: 173 AN XY: 134292

Gnomad AFR exome AF: 0.0162

Gnomad AMR exome AF: 0.00233

Gnomad ASJ exome AF: 0.000400

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000661

Gnomad FIN exome AF: 0.0000929

Gnomad NFE exome AF: 0.000499

Gnomad OTH exome AF: 0.00181

GnomAD4 exome AF: 0.000746 AC: 1089 AN: 1460450 Hom.: 9 Cov.: 31 AF XY: 0.000625 AC XY: 454 AN XY: 726356

Gnomad4 AFR exome AF: 0.0185

Gnomad4 AMR exome AF: 0.00209

Gnomad4 ASJ exome AF: 0.000153

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000698

Gnomad4 FIN exome AF: 0.0000375

Gnomad4 NFE exome AF: 0.000252

Gnomad4 OTH exome AF: 0.00128

GnomAD4 genome AF: 0.00476 AC: 725 AN: 152270 Hom.: 8 Cov.: 32 AF XY: 0.00439 AC XY: 327 AN XY: 74460

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.00118

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000500

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00265 Hom.: 1

Bravo AF: 0.00556

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Jul 29, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Nov 09, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CACNA1C-related disorder Benign:1

Jan 13, 2020

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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). -

Long QT syndrome Benign:1

Jan 31, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Benign:1

Jun 14, 2016

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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	-0.79
CADD	Benign	4.0
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs188224114; hg19: chr12-2717707;