rs2239106

Variant names:

• chr12-2517712-A-T
• rs2239106
• NM_000719.7:c.1390+4728A>T

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+4728A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,192 control chromosomes in the GnomAD database, including 2,909 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 0.17 (2909 hom., cov: 33)
• Consequence: CACNA1C NM_000719.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1390+4728A>T		intron_variant	Intron 9 of 46	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1390+4728A>T		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+4728A>T		intron_variant	Intron 9 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.1390+4728A>T		intron_variant	Intron 9 of 46	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.1480+4728A>T		intron_variant	Intron 9 of 49			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.1390+4728A>T		intron_variant	Intron 9 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1390+4728A>T		intron_variant	Intron 9 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.1480+4728A>T		intron_variant	Intron 9 of 47			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.1390+4728A>T		intron_variant	Intron 9 of 48	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1390+4728A>T		intron_variant	Intron 9 of 47	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.1390+4728A>T		intron_variant	Intron 9 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.1480+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.1480+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.1480+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.1480+4728A>T		intron_variant	Intron 9 of 46			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.1390+4728A>T		intron_variant	Intron 9 of 47	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.1390+4728A>T		intron_variant	Intron 9 of 47	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1390+4728A>T		intron_variant	Intron 9 of 47	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.1390+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1390+4728A>T		intron_variant	Intron 9 of 45	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1390+4728A>T		intron_variant	Intron 9 of 45	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1390+4728A>T		intron_variant	Intron 9 of 45	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.1390+4728A>T		intron_variant	Intron 9 of 46	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.1390+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.1381+4728A>T		intron_variant	Intron 9 of 46			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1390+4728A>T		intron_variant	Intron 9 of 45			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.1113+24326A>T		intron_variant	Intron 7 of 26	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26572 AN: 152074 Hom.: 2897 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0584

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.175 AC: 26609 AN: 152192 Hom.: 2909 Cov.: 33 AF XY: 0.175 AC XY: 13010 AN XY: 74412

African (AFR) AF: 0.293 AC: 12149 AN: 41490

American (AMR) AF: 0.215 AC: 3286 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3466

East Asian (EAS) AF: 0.241 AC: 1246 AN: 5164

South Asian (SAS) AF: 0.151 AC: 728 AN: 4818

European-Finnish (FIN) AF: 0.0584 AC: 620 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7565 AN: 68028

Other (OTH) AF: 0.164 AC: 346 AN: 2114

Alfa AF: 0.142 Hom.: 257

Bravo AF: 0.191

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.45
PhyloP100		-0.88
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: rs2239106; hg19: chr12-2626878;