chr12-2679735-G-A

Position:

• chr12-2679735-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2 BP4_Strong BP6_Very_Strong BA1

The NM_000719.7(CACNA1C):​c.5383G>A​(p.Gly1795Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 1,604,226 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.015 (63 hom., cov: 33)
  • Exomes 𝑓: 0.0016 (57 hom.)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 2.96

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]

CACNA1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1C. . Gene score misZ 6.4654 (greater than the threshold 3.09). Trascript score misZ 7.2674 (greater than threshold 3.09). GenCC has associacion of gene with intellectual disability, neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures, Brugada syndrome, long QT syndrome, short QT syndrome, long qt syndrome 8, Timothy syndrome, Brugada syndrome 3.
• BP4: Computational evidence support a benign effect (MetaRNN=0.0023810267).
• BP6: Variant 12-2679735-G-A is Benign according to our data. Variant chr12-2679735-G-A is described in ClinVar as [Benign]. Clinvar id is 191565.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-2679735-G-A is described in Lovd as [Benign].
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.5617G>A	p.Gly1873Arg	missense_variant	44/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.5383G>A	p.Gly1795Arg	missense_variant	42/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.5350G>A	p.Gly1784Arg	missense_variant	41/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.5548G>A	p.Gly1850Arg	missense_variant	43/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.5527G>A	p.Gly1843Arg	missense_variant	44/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.5506G>A	p.Gly1836Arg	missense_variant	42/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.5383G>A	p.Gly1795Arg	missense_variant	42/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.5383G>A	p.Gly1795Arg	missense_variant	42/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.5473G>A	p.Gly1825Arg	missense_variant	42/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.5473G>A	p.Gly1825Arg	missense_variant	42/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.5473G>A	p.Gly1825Arg	missense_variant	42/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.5473G>A	p.Gly1825Arg	missense_variant	42/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.5467G>A	p.Gly1823Arg	missense_variant	43/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.5458G>A	p.Gly1820Arg	missense_variant	43/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.5443G>A	p.Gly1815Arg	missense_variant	43/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.5440G>A	p.Gly1814Arg	missense_variant	42/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.5440G>A	p.Gly1814Arg	missense_variant	42/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.5440G>A	p.Gly1814Arg	missense_variant	42/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.5434G>A	p.Gly1812Arg	missense_variant	42/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.5425G>A	p.Gly1809Arg	missense_variant	42/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.5407G>A	p.Gly1803Arg	missense_variant	41/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.5407G>A	p.Gly1803Arg	missense_variant	41/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.5401G>A	p.Gly1801Arg	missense_variant	41/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.5383G>A	p.Gly1795Arg	missense_variant	42/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.5383G>A	p.Gly1795Arg	missense_variant	42/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.5374G>A	p.Gly1792Arg	missense_variant	42/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.5350G>A	p.Gly1784Arg	missense_variant	41/46			ENSP00000507309.1

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2254 AN: 152142 Hom.: 62 Cov.: 33

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00497

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.00907

GnomAD3 exomes AF: 0.00368 AC: 835 AN: 226606 Hom.: 24 AF XY: 0.00287 AC XY: 354 AN XY: 123184

Gnomad AFR exome AF: 0.0538

Gnomad AMR exome AF: 0.00342

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000700

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000140

Gnomad OTH exome AF: 0.00194

GnomAD4 exome AF: 0.00159 AC: 2306 AN: 1451966 Hom.: 57 Cov.: 34 AF XY: 0.00137 AC XY: 985 AN XY: 721406

Gnomad4 AFR exome AF: 0.0546

Gnomad4 AMR exome AF: 0.00349

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000118

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000120

Gnomad4 OTH exome AF: 0.00310

GnomAD4 genome AF: 0.0148 AC: 2261 AN: 152260 Hom.: 63 Cov.: 33 AF XY: 0.0147 AC XY: 1092 AN XY: 74444

Gnomad4 AFR AF: 0.0517

Gnomad4 AMR AF: 0.00497

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.00898

Alfa AF: 0.00838 Hom.: 11

Bravo AF: 0.0171

ESP6500AA AF: 0.0438 AC: 176

ESP6500EA AF: 0.000240 AC: 2

ExAC AF: 0.00399 AC: 481

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 07, 2023	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified Benign:2

Benign, criteria provided, single submitter	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jun 24, 2013	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Long QT syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Cardiovascular phenotype Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 15, 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.31	N
MetaRNN	Benign	0.0024	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.24	T
MutationAssessor	Benign	1.7	.;.;.;.;.;.;.;.;.;.;L;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI	Uncertain	0.48	T
PROVEAN	Benign	-2.0	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;D;N;D;.
REVEL	Benign	0.22
Sift	Benign	0.054	T;T;T;T;T;T;D;D;T;T;T;T;T;D;T;D;D;D;T;D;D;D;.
Sift4G	Benign	0.23	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;D;T
Polyphen		0.18, 0.0030, 0.79, 0.0, 0.97, 0.0010, 0.010, 0.37, 0.087, 0.0050, 0.98, 0.014	.;B;B;P;B;B;D;B;B;B;B;B;B;B;B;.;D;B;.;.;.;B;.
Vest4		0.33
MutPred		0.33		.;.;.;.;.;.;.;.;.;.;Gain of catalytic residue at E1840 (P = 0.0012);.;.;.;.;.;.;.;.;.;.;.;.;
MVP		0.61
MPC		0.23
ClinPred		0.0052	T
GERP RS		3.0
gMVP		0.37

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: rs111298509; hg19: chr12-2788901;