rs369673473

Variant names:

• chr12-2449035-C-A
• NM_000719.7:c.537C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-2449035-C-A
• chr12-2449035-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Moderate BP6_Moderate BP7

The NM_000719.7(CACNA1C):​c.537C>A​(p.Ile179Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,898 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 (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0690

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]

ENSG00000285734 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BP6: Variant 12-2449035-C-A is Benign according to our data. Variant chr12-2449035-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2716646.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.069 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.627C>A	p.Ile209Ile	synonymous_variant	Exon 4 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.537C>A	p.Ile179Ile	synonymous_variant	Exon 4 of 46			ENSP00000507309.1
CACNA1C	ENST00000682152.1	c.486C>A	p.Ile162Ile	synonymous_variant	Exon 3 of 6			ENSP00000506759.1
CACNA1C	ENST00000480911.6	n.537C>A		non_coding_transcript_exon_variant	Exon 4 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.90e-7 AC: 1 AN: 1448898 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 720226

Gnomad4 AFR exome AF: 0.0000300

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Long QT syndrome Benign:1

Dec 28, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	8.4
DANN	Benign	0.81

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-2558201; COSMIC: COSV59741405;