12-2585466-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_000719.7(CACNA1C):c.2430G>T(p.Thr810Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000281 in 1,425,118 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 (★). Synonymous variant affecting the same amino acid position (i.e. T810T) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

CACNA1C
NM_000719.7 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.87

Publications

0 publications found

Variant links:

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 Gene-Disease associations (from GenCC):

Timothy syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures
Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics
long QT syndrome
Inheritance: AD Classification: MODERATE Submitted by: ClinGen
long QT syndrome 8
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
Brugada syndrome
Inheritance: AD Classification: SUPPORTIVE, NO_KNOWN Submitted by: Orphanet, ClinGen
Brugada syndrome 3
Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
intellectual disability
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
short QT syndrome
Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, ClinGen

CACNA1C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 12-2585466-G-T is Benign according to our data. Variant chr12-2585466-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2731169.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.87 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
CACNA1C	ENST00000399603.6 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1 link	c.2520G>T	p.Thr840Thr	synonymous_variant	Exon 17 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1 link	c.2595G>T	p.Thr865Thr	synonymous_variant	Exon 18 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1 link	c.2520G>T	p.Thr840Thr	synonymous_variant	Exon 17 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1 link	c.2520G>T	p.Thr840Thr	synonymous_variant	Exon 17 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1 link	c.2520G>T	p.Thr840Thr	synonymous_variant	Exon 17 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1 link	c.2520G>T	p.Thr840Thr	synonymous_variant	Exon 17 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10 link	c.2505G>T	p.Thr835Thr	synonymous_variant	Exon 18 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1 link	c.2505G>T	p.Thr835Thr	synonymous_variant	Exon 18 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1 link	c.2421G>T	p.Thr807Thr	synonymous_variant	Exon 17 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1 link	c.2430G>T	p.Thr810Thr	synonymous_variant	Exon 17 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6 link	n.*1037G>T		non_coding_transcript_exon_variant	Exon 15 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6 link	n.*1037G>T		3_prime_UTR_variant	Exon 15 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000107

AC:

AN:

186368

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000257

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000281

AC:

AN:

1425118

Hom.:

Cov.:

AF XY:

0.00000142

AC XY:

AN XY:

705758

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

32964

American (AMR)

AF:

0.00

AC:

AN:

38388

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25512

East Asian (EAS)

AF:

0.00

AC:

AN:

38174

South Asian (SAS)

AF:

0.00

AC:

AN:

81844

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50866

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5642

European-Non Finnish (NFE)

AF:

0.00000366

AC:

AN:

1092768

Other (OTH)

AF:

0.00

AC:

AN:

58960

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000283

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Long QT syndrome

Benign:1

May 29, 2024

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

-0.88

CADD

Benign

0.016

(source)

DANN

Benign

0.47

PhyloP100

-2.9

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over