12-2651762-C-T

Variant names:

• chr12-2651762-C-T
• rs765091519
• NM_000719.7:c.4068C>T

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Moderate BP6_Very_Strong BP7 BS2

The NM_000719.7(CACNA1C):​c.4068C>T​(p.Ser1356Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000785 in 1,605,316 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1356S) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000080 (0 hom.)
• Consequence: CACNA1C NM_000719.7 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 0.579
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• Timothy syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics
• long QT syndrome

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• long QT syndrome 8

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• Brugada syndrome

  Inheritance: AD Classification: SUPPORTIVE, NO_KNOWN Submitted by: Orphanet, ClinGen
• Brugada syndrome 3

  Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• short QT syndrome

  Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, ClinGen

ACMG classification

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP6: Variant 12-2651762-C-T is Benign according to our data. Variant chr12-2651762-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 527030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.579 with no splicing effect.
• BS2: High AC in GnomAd4 at 10 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.4302C>T	p.Ser1434Ser	synonymous_variant	Exon 34 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.4035C>T	p.Ser1345Ser	synonymous_variant	Exon 31 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.4233C>T	p.Ser1411Ser	synonymous_variant	Exon 33 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.4212C>T	p.Ser1404Ser	synonymous_variant	Exon 34 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.4134C>T	p.Ser1378Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.4158C>T	p.Ser1386Ser	synonymous_variant	Exon 32 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.4158C>T	p.Ser1386Ser	synonymous_variant	Exon 32 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.4158C>T	p.Ser1386Ser	synonymous_variant	Exon 32 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.4158C>T	p.Ser1386Ser	synonymous_variant	Exon 32 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.4152C>T	p.Ser1384Ser	synonymous_variant	Exon 33 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.4143C>T	p.Ser1381Ser	synonymous_variant	Exon 33 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.4128C>T	p.Ser1376Ser	synonymous_variant	Exon 33 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.4119C>T	p.Ser1373Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.4110C>T	p.Ser1370Ser	synonymous_variant	Exon 32 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.4035C>T	p.Ser1345Ser	synonymous_variant	Exon 31 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.4035C>T	p.Ser1345Ser	synonymous_variant	Exon 31 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.4029C>T	p.Ser1343Ser	synonymous_variant	Exon 31 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.4068C>T	p.Ser1356Ser	synonymous_variant	Exon 32 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.4059C>T	p.Ser1353Ser	synonymous_variant	Exon 32 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.4035C>T	p.Ser1345Ser	synonymous_variant	Exon 31 of 46			ENSP00000507309.1

Frequencies

GnomAD3 genomes AF: 0.0000661 AC: 10 AN: 151370 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000657

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000616 AC: 15 AN: 243692 AF XY: 0.0000908

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000127

Gnomad OTH exome AF: 0.000169

GnomAD4 exome AF: 0.0000798 AC: 116 AN: 1453946 Hom.: 0 Cov.: 33 AF XY: 0.0000692 AC XY: 50 AN XY: 722026

African (AFR) AF: 0.00 AC: 0 AN: 33384

American (AMR) AF: 0.00 AC: 0 AN: 44484

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25794

East Asian (EAS) AF: 0.00 AC: 0 AN: 39556

South Asian (SAS) AF: 0.00 AC: 0 AN: 85522

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53060

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5712

European-Non Finnish (NFE) AF: 0.000104 AC: 115 AN: 1106378

Other (OTH) AF: 0.0000167 AC: 1 AN: 60056

GnomAD4 genome AF: 0.0000661 AC: 10 AN: 151370 Hom.: 0 Cov.: 31 AF XY: 0.0000406 AC XY: 3 AN XY: 73936

African (AFR) AF: 0.0000245 AC: 1 AN: 40882

American (AMR) AF: 0.0000657 AC: 1 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00 AC: 0 AN: 4778

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 67954

Other (OTH) AF: 0.00 AC: 0 AN: 2084

Alfa AF: 0.0000762 Hom.: 0

Bravo AF: 0.0000378

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

May 01, 2019

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not specified Benign:1

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

CACNA1C-related disorder Benign:1

Aug 19, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely 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

Dec 25, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Cardiovascular phenotype Benign:1

Feb 01, 2019

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely 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	-0.33
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.58

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

Other links and lift over

dbSNP: rs765091519; hg19: chr12-2760928;