rs750329281

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_000719.7(CACNA1C):c.1491C>T(p.Ile497Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,700 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 (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

CACNA1C
NM_000719.7 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.67

Publications

1 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: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 12-2556960-C-T is Benign according to our data. Variant chr12-2556960-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 456946.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.67 with no splicing effect.

BS2

High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
CACNA1C	ENST00000399603.6 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1 link	c.1581C>T	p.Ile527Ile	synonymous_variant	Exon 11 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1 link	c.1656C>T	p.Ile552Ile	synonymous_variant	Exon 12 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1 link	c.1581C>T	p.Ile527Ile	synonymous_variant	Exon 11 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1 link	c.1581C>T	p.Ile527Ile	synonymous_variant	Exon 11 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1 link	c.1581C>T	p.Ile527Ile	synonymous_variant	Exon 11 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1 link	c.1581C>T	p.Ile527Ile	synonymous_variant	Exon 11 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10 link	c.1566C>T	p.Ile522Ile	synonymous_variant	Exon 12 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1 link	c.1566C>T	p.Ile522Ile	synonymous_variant	Exon 12 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1 link	c.1482C>T	p.Ile494Ile	synonymous_variant	Exon 11 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1 link	c.1491C>T	p.Ile497Ile	synonymous_variant	Exon 11 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6 link	n.*98C>T		non_coding_transcript_exon_variant	Exon 9 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6 link	n.*98C>T		3_prime_UTR_variant	Exon 9 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000401

AC:

AN:

249268

AF XY:

0.00000740

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:

0.00000885

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000411

AC:

AN:

1460700

Hom.:

Cov.:

AF XY:

0.00000550

AC XY:

AN XY:

726732

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33466

American (AMR)

AF:

0.00

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26130

East Asian (EAS)

AF:

0.00

AC:

AN:

39696

South Asian (SAS)

AF:

0.00

AC:

AN:

86242

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53390

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00000540

AC:

AN:

1110952

Other (OTH)

AF:

0.00

AC:

AN:

60336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000468

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Long QT syndrome

Benign:1

Dec 10, 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

-0.27

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

1.7

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

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over