NM_000719.7:c.1125C>A

Variant names:

• chr12-2504853-C-A
• NM_000719.7:c.1125C>A

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_000719.7(CACNA1C):​c.1125C>A​(p.Ala375Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000007 in 1,427,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

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 Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BP7: Synonymous conserved (PhyloP=1.9 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1217+314C>A		intron_variant	Intron 8 of 46	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399655.6	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.1215C>A	p.Ala405Ala	synonymous_variant	Exon 8 of 50			ENSP00000507184.1
CACNA1C	ENST00000347598.9	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399638.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399644.5	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000683482.1	c.1116C>A	p.Ala372Ala	synonymous_variant	Exon 8 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1125C>A	p.Ala375Ala	synonymous_variant	Exon 8 of 46			ENSP00000507309.1
CACNA1C	ENST00000399603.6	c.1217+314C>A		intron_variant	Intron 8 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000406454.8	c.1217+314C>A		intron_variant	Intron 8 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1217+314C>A		intron_variant	Intron 8 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.1307+314C>A		intron_variant	Intron 8 of 47			ENSP00000507867.1
CACNA1C	ENST00000399617.6	c.1217+314C>A		intron_variant	Intron 8 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.1307+314C>A		intron_variant	Intron 8 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.1307+314C>A		intron_variant	Intron 8 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.1307+314C>A		intron_variant	Intron 8 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.1307+314C>A		intron_variant	Intron 8 of 46			ENSP00000506882.1
CACNA1C	ENST00000399641.6	c.1217+314C>A		intron_variant	Intron 8 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000682835.1	c.1217+314C>A		intron_variant	Intron 8 of 46			ENSP00000507282.1
CACNA1C	ENST00000480911.6	n.1113+11467C>A		intron_variant	Intron 7 of 26	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.00e-7 AC: 1 AN: 1427806 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 712636

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	12
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: chr12-2614019;