chr12-2547459-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2

The ENST00000683824.1(CACNA1C):c.1490C>T(p.Pro497Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 779,644 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 2 hom., cov: 33)

Exomes 𝑓: 0.00055 ( 1 hom. )

Consequence

CACNA1C
ENST00000683824.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:1

Conservation

PhyloP100: 1.42

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

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: 7.3124 (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.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057228208).

BP6

Variant 12-2547459-C-T is Benign according to our data. Variant chr12-2547459-C-T is described in ClinVar as [Benign]. Clinvar id is 191564.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00453 (690/152208) while in subpopulation AFR AF= 0.0159 (661/41514). AF 95% confidence interval is 0.0149. There are 2 homozygotes in gnomad4. There are 334 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 690 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	ENST00000399655.6	NP_000710.5	Q13936-12
CACNA1C	NM_001167623.2 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	ENST00000399603.6	NP_001161095.1	Q13936-37

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CACNA1C	ENST00000683824.1 link	c.1490C>T	p.Pro497Leu	missense_variant	Exon 10 of 48			ENSP00000507867.1	A0A804HKC4
CACNA1C	ENST00000335762.10 link	c.1400C>T	p.Pro467Leu	missense_variant	Exon 10 of 48	5		ENSP00000336982.5	F5H522
CACNA1C	ENST00000682336.1 link	c.1400C>T	p.Pro467Leu	missense_variant	Exon 10 of 47			ENSP00000507898.1	A0A804HKE9
CACNA1C	ENST00000399603.6 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	5	NM_001167623.2	ENSP00000382512.1	Q13936-37
CACNA1C	ENST00000399655.6 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1	NM_000719.7	ENSP00000382563.1	Q13936-12
CACNA1C	ENST00000682544.1 link	c.1481-2484C>T		intron_variant	Intron 9 of 49			ENSP00000507184.1	A0A804HIR0
CACNA1C	ENST00000406454.8 link	c.1391-2484C>T		intron_variant	Intron 9 of 47	5		ENSP00000385896.3	F5GY28
CACNA1C	ENST00000399634.6 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	5		ENSP00000382542.2	E9PDI6
CACNA1C	ENST00000347598.9 link	c.1391-2484C>T		intron_variant	Intron 9 of 48	1		ENSP00000266376.6	Q13936-11
CACNA1C	ENST00000344100.7 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000341092.3	Q13936-14
CACNA1C	ENST00000327702.12 link	c.1391-2484C>T		intron_variant	Intron 9 of 47	1		ENSP00000329877.7	A0A0A0MR67
CACNA1C	ENST00000399617.6 link	c.1391-2484C>T		intron_variant	Intron 9 of 47	5		ENSP00000382526.1	A0A0A0MSA1
CACNA1C	ENST00000682462.1 link	c.1481-2484C>T		intron_variant	Intron 9 of 46			ENSP00000507105.1	A0A804HIJ8
CACNA1C	ENST00000683781.1 link	c.1481-2484C>T		intron_variant	Intron 9 of 46			ENSP00000507434.1	A0A804HJB6
CACNA1C	ENST00000683840.1 link	c.1481-2484C>T		intron_variant	Intron 9 of 46			ENSP00000507612.1	A0A804HJR1
CACNA1C	ENST00000683956.1 link	c.1481-2484C>T		intron_variant	Intron 9 of 46			ENSP00000506882.1	A0A804HI37
CACNA1C	ENST00000399638.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 47	1		ENSP00000382547.1	Q13936-31
CACNA1C	ENST00000399606.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 47	1		ENSP00000382515.1	Q13936-30
CACNA1C	ENST00000399621.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382530.1	Q13936-24
CACNA1C	ENST00000399637.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382546.1	Q13936-27
CACNA1C	ENST00000402845.7 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000385724.3	Q13936-13
CACNA1C	ENST00000399629.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382537.1	Q13936-32
CACNA1C	ENST00000399591.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 45	1		ENSP00000382500.1	Q13936-29
CACNA1C	ENST00000399595.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 45	1		ENSP00000382504.1	Q13936-25
CACNA1C	ENST00000399649.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 45	1		ENSP00000382557.1	Q13936-15
CACNA1C	ENST00000399597.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382506.1	Q13936-22
CACNA1C	ENST00000399601.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382510.1	Q13936-20
CACNA1C	ENST00000399641.6 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382549.1	Q13936-23
CACNA1C	ENST00000399644.5 link	c.1391-2484C>T		intron_variant	Intron 9 of 46	1		ENSP00000382552.1	Q13936-21
CACNA1C	ENST00000682835.1 link	c.1391-2484C>T		intron_variant	Intron 9 of 46			ENSP00000507282.1	A0A804HIZ0
CACNA1C	ENST00000683482.1 link	c.1382-2484C>T		intron_variant	Intron 9 of 46			ENSP00000507169.1	Q13936-35
CACNA1C	ENST00000682686.1 link	c.1391-2484C>T		intron_variant	Intron 9 of 45			ENSP00000507309.1	Q13936-19
CACNA1C	ENST00000480911.6 link	n.1114-2484C>T		intron_variant	Intron 7 of 26	5		ENSP00000437936.2	F5H638

Frequencies

GnomAD3 genomes

AF:

0.00455

AC:

692

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0160

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00111

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.000961

AC:

232

AN:

241472

Hom.:

AF XY:

0.000792

AC XY:

105

AN XY:

132580

show subpopulations

Gnomad AFR exome

AF:

0.0148

Gnomad AMR exome

AF:

0.000436

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000466

Gnomad OTH exome

AF:

0.000167

GnomAD4 exome

AF:

0.000548

AC:

344

AN:

627436

Hom.:

Cov.:

AF XY:

0.000445

AC XY:

152

AN XY:

341848

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.000777

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000430

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000400

Gnomad4 OTH exome

AF:

0.000907

GnomAD4 genome

AF:

0.00453

AC:

690

AN:

152208

Hom.:

Cov.:

AF XY:

0.00449

AC XY:

334

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0159

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00150

Hom.:

Bravo

AF:

0.00473

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0120

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00116

AC:

135

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Jun 24, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.81

DEOGEN2

Benign

0.0074

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.078

FATHMM_MKL

Uncertain

0.81

MetaRNN

Benign

0.0057

MetaSVM

Uncertain

-0.012

PROVEAN

Benign

0.25

REVEL

Benign

0.18

Sift

Benign

0.32

Sift4G

Benign

0.42

Vest4

0.30

MVP

0.61

ClinPred

0.015

GERP RS

3.2

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over