chr12-2605744-G-A

Position:

• chr12-2605744-G-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.3114G>A​(p.Leu1038Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L1038L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1C NM_000719.7 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65

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-AS3 (HGNC:40117): (CACNA1C antisense RNA 3)

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=-0.41).
• BP7: Synonymous conserved (PhyloP=2.65 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3264G>A	p.Leu1088Leu	synonymous_variant	25/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3279G>A	p.Leu1093Leu	synonymous_variant	25/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3174G>A	p.Leu1058Leu	synonymous_variant	25/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3204G>A	p.Leu1068Leu	synonymous_variant	24/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3204G>A	p.Leu1068Leu	synonymous_variant	24/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3204G>A	p.Leu1068Leu	synonymous_variant	24/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3204G>A	p.Leu1068Leu	synonymous_variant	24/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3189G>A	p.Leu1063Leu	synonymous_variant	25/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3174G>A	p.Leu1058Leu	synonymous_variant	25/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3189G>A	p.Leu1063Leu	synonymous_variant	25/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3105G>A	p.Leu1035Leu	synonymous_variant	24/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3114G>A	p.Leu1038Leu	synonymous_variant	24/46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1721G>A		non_coding_transcript_exon_variant	22/27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1721G>A		3_prime_UTR_variant	22/27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	11
DANN	Benign	0.86

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: rs114139824; hg19: chr12-2714910;