rs2239104

Variant names:

• chr12-2514377-T-G
• rs2239104
• NM_000719.7:c.1390+1393T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000719.7(CACNA1C):​c.1390+1393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,200 control chromosomes in the GnomAD database, including 4,031 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (4031 hom., cov: 33)
• Consequence: CACNA1C NM_000719.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 3 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1390+1393T>G		intron_variant	Intron 9 of 46	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1390+1393T>G		intron_variant	Intron 9 of 46	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.1390+1393T>G		intron_variant	Intron 9 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.1390+1393T>G		intron_variant	Intron 9 of 46	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.1480+1393T>G		intron_variant	Intron 9 of 49			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.1390+1393T>G		intron_variant	Intron 9 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1390+1393T>G		intron_variant	Intron 9 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.1480+1393T>G		intron_variant	Intron 9 of 47			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.1390+1393T>G		intron_variant	Intron 9 of 48	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1390+1393T>G		intron_variant	Intron 9 of 47	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.1390+1393T>G		intron_variant	Intron 9 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.1480+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.1480+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.1480+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.1480+1393T>G		intron_variant	Intron 9 of 46			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.1390+1393T>G		intron_variant	Intron 9 of 47	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.1390+1393T>G		intron_variant	Intron 9 of 47	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1390+1393T>G		intron_variant	Intron 9 of 47	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.1390+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1390+1393T>G		intron_variant	Intron 9 of 45	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1390+1393T>G		intron_variant	Intron 9 of 45	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1390+1393T>G		intron_variant	Intron 9 of 45	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.1390+1393T>G		intron_variant	Intron 9 of 46	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.1390+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.1381+1393T>G		intron_variant	Intron 9 of 46			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1390+1393T>G		intron_variant	Intron 9 of 45			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.1113+20991T>G		intron_variant	Intron 7 of 26	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29393 AN: 152082 Hom.: 4010 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.178

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.194 AC: 29451 AN: 152200 Hom.: 4031 Cov.: 33 AF XY: 0.191 AC XY: 14214 AN XY: 74436

African (AFR) AF: 0.383 AC: 15870 AN: 41486

American (AMR) AF: 0.140 AC: 2134 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5176

South Asian (SAS) AF: 0.158 AC: 764 AN: 4830

European-Finnish (FIN) AF: 0.0578 AC: 614 AN: 10620

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7596 AN: 68010

Other (OTH) AF: 0.177 AC: 374 AN: 2116

Alfa AF: 0.141 Hom.: 1565

Bravo AF: 0.210

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.9
DANN	Benign	0.79
PhyloP100		0.017
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2239104; hg19: chr12-2623543;