rs370630496

Variant names:

• chr12-2651630-C-G
• rs370630496
• ENST00000344100.7:c.4002C>G

Your query was ambiguous. Multiple possible variants found:

• chr12-2651630-C-G
• chr12-2651630-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP2

The NM_001129829.2(CACNA1C):​c.4002C>G​(p.Asp1334Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1334N) has been classified as Likely benign.

• Frequency: Genomes: 𝑓 0.000013 (0 hom., cov: 32)
• Consequence: CACNA1C NM_001129829.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.180

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 Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the CACNA1C gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 91 curated benign missense variants. Gene score misZ: 6.4654 (above the threshold of 3.09). Trascript score misZ: 7.1751 (above the threshold of 3.09). GenCC associations: The gene is linked to intellectual disability, neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures, Brugada syndrome, long QT syndrome, short QT syndrome, long qt syndrome 8, Timothy syndrome, Brugada syndrome 3.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3946-10C>G		intron_variant	Intron 31 of 46	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3946-10C>G		intron_variant	Intron 31 of 46	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000344100.7	c.4002C>G	p.Asp1334Glu	missense_variant	Exon 32 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000399603.6	c.3946-10C>G		intron_variant	Intron 31 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3946-10C>G		intron_variant	Intron 31 of 46	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.4180-10C>G		intron_variant	Intron 33 of 49			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3946-10C>G		intron_variant	Intron 31 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3913-10C>G		intron_variant	Intron 30 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.4111-10C>G		intron_variant	Intron 32 of 47			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.4090-10C>G		intron_variant	Intron 33 of 48	1		ENSP00000266376.6
CACNA1C	ENST00000327702.12	c.3946-10C>G		intron_variant	Intron 31 of 47	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3946-10C>G		intron_variant	Intron 31 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.4036-10C>G		intron_variant	Intron 31 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.4036-10C>G		intron_variant	Intron 31 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.4036-10C>G		intron_variant	Intron 31 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.4036-10C>G		intron_variant	Intron 31 of 46			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.4030-10C>G		intron_variant	Intron 32 of 47	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.4021-10C>G		intron_variant	Intron 32 of 47	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.4006-10C>G		intron_variant	Intron 32 of 47	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3997-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3988-10C>G		intron_variant	Intron 31 of 46			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3913-10C>G		intron_variant	Intron 30 of 45	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3913-10C>G		intron_variant	Intron 30 of 45	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3907-10C>G		intron_variant	Intron 30 of 45	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3946-10C>G		intron_variant	Intron 31 of 46	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3946-10C>G		intron_variant	Intron 31 of 46			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3937-10C>G		intron_variant	Intron 31 of 46			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3913-10C>G		intron_variant	Intron 30 of 45			ENSP00000507309.1

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152150 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152150 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74330

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Long QT syndrome Uncertain:1

Mar 18, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 411722). This variant has not been reported in the literature in individuals affected with CACNA1C-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 31 of the CACNA1C gene. It does not directly change the encoded amino acid sequence of the CACNA1C protein. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	23
DANN	Benign	0.51
Eigen	Benign	-0.84
Eigen_PC	Benign	-0.74
FATHMM_MKL	Benign	0.63	D
M_CAP	Benign	0.084	D
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.40	T
PROVEAN	Benign	-0.76	N
REVEL	Uncertain	0.35
Sift	Benign	0.52	T
Sift4G	Benign	0.71	T
Polyphen		0.0	B
Vest4		0.087
MutPred		0.49		Gain of catalytic residue at P1330 (P = 0.0016);
MVP		0.61
ClinPred		0.054	T
GERP RS		-0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.46		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.46		Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs370630496; hg19: chr12-2760796;