12-2069379-A-G

Variant names:

• chr12-2069379-A-G
• rs2238017
• NM_000719.7:c.49+15768A>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.49+15768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,996 control chromosomes in the GnomAD database, including 16,370 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 0.45 (16370 hom., cov: 32)
• Consequence: CACNA1C NM_000719.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.49+15768A>G		intron_variant	Intron 1 of 46	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.49+15768A>G		intron_variant	Intron 1 of 46	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.49+15768A>G		intron_variant	Intron 1 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.49+15768A>G		intron_variant	Intron 1 of 46	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.140-45845A>G		intron_variant	Intron 1 of 49			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.49+15768A>G		intron_variant	Intron 1 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.49+15768A>G		intron_variant	Intron 1 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.140-45845A>G		intron_variant	Intron 1 of 47			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.49+15768A>G		intron_variant	Intron 1 of 48	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.49+15768A>G		intron_variant	Intron 1 of 47	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.49+15768A>G		intron_variant	Intron 1 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.140-45845A>G		intron_variant	Intron 1 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.140-45845A>G		intron_variant	Intron 1 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.140-45845A>G		intron_variant	Intron 1 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.140-45845A>G		intron_variant	Intron 1 of 46			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.49+15768A>G		intron_variant	Intron 1 of 47	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.49+15768A>G		intron_variant	Intron 1 of 47	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.49+15768A>G		intron_variant	Intron 1 of 47	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.49+15768A>G		intron_variant	Intron 1 of 46			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.49+15768A>G		intron_variant	Intron 1 of 45	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.49+15768A>G		intron_variant	Intron 1 of 45	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.49+15768A>G		intron_variant	Intron 1 of 45	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.49+15768A>G		intron_variant	Intron 1 of 46	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.49+15768A>G		intron_variant	Intron 1 of 46			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.49+15768A>G		intron_variant	Intron 1 of 46			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.49+15768A>G		intron_variant	Intron 1 of 45			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.49+15768A>G		intron_variant	Intron 1 of 26	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67997 AN: 151878 Hom.: 16334 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.448 AC: 68097 AN: 151996 Hom.: 16370 Cov.: 32 AF XY: 0.462 AC XY: 34297 AN XY: 74280

African (AFR) AF: 0.592 AC: 24538 AN: 41456

American (AMR) AF: 0.468 AC: 7141 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1018 AN: 3466

East Asian (EAS) AF: 0.706 AC: 3639 AN: 5156

South Asian (SAS) AF: 0.521 AC: 2511 AN: 4822

European-Finnish (FIN) AF: 0.492 AC: 5202 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22631 AN: 67954

Other (OTH) AF: 0.437 AC: 924 AN: 2114

Alfa AF: 0.363 Hom.: 17353

Bravo AF: 0.451

Asia WGS AF: 0.626 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		0.082
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: rs2238017; hg19: chr12-2178545;