12-2053563-A-C

Variant names:

• chr12-2053563-A-C
• rs931964122
• NM_000719.7:c.1A>C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PVS1_Supporting BS2

The NM_000719.7(CACNA1C):​c.1A>C​(p.Met1?) variant causes a initiator codon change. The variant allele was found at a frequency of 0.00000692 in 1,444,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000069 (0 hom.)
• Consequence: CACNA1C NM_000719.7 initiator_codon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.83

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 -3 ACMG points.

• PVS1: Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 8 codons. Genomic position: 2053584. Lost 0.003 part of the original CDS.
• BS2: High AC in GnomAdExome4 at 10 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000406454.8	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000347598.9	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000399638.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 46			ENSP00000507309.1
CACNA1C	ENST00000682544.1	c.140-61661A>C		intron_variant	Intron 1 of 49			ENSP00000507184.1
CACNA1C	ENST00000683824.1	c.140-61661A>C		intron_variant	Intron 1 of 47			ENSP00000507867.1
CACNA1C	ENST00000682462.1	c.140-61661A>C		intron_variant	Intron 1 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.140-61661A>C		intron_variant	Intron 1 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.140-61661A>C		intron_variant	Intron 1 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.140-61661A>C		intron_variant	Intron 1 of 46			ENSP00000506882.1
CACNA1C	ENST00000480911.6	n.1A>C		non_coding_transcript_exon_variant	Exon 1 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000692 AC: 10 AN: 1444082 Hom.: 0 Cov.: 32 AF XY: 0.00000558 AC XY: 4 AN XY: 716624

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000906

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual disability Uncertain:1

Sep 10, 2020

Diagnostic Laboratory, Strasbourg University Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.42
CADD	Benign	21
DANN	Benign	0.92
DEOGEN2	Benign	0.011	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Benign	-0.071
Eigen_PC	Benign	-0.025
FATHMM_MKL	Benign	0.66	D
M_CAP	Pathogenic	0.90	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.78	D
PROVEAN	Benign	-0.42	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL	Uncertain	0.64
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen		0.10, 0.011, 0.26	.;B;.;B;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;.;.;.;.
Vest4		0.85
MutPred		0.98		Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);Gain of catalytic residue at T6 (P = 0.095);
MVP		0.99
ClinPred		0.99	D
GERP RS		3.0
gMVP		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

Publications

LitVar

Other links and lift over

dbSNP: rs931964122; hg19: chr12-2162729;