NM_000719.7:c.4828+164T>C

Variant names:

• chr12-2674806-T-C
• rs2302729
• NM_000719.7:c.4828+164T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000719.7(CACNA1C):​c.4828+164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,134 control chromosomes in the GnomAD database, including 40,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.71 (40573 hom., cov: 33)
• Consequence: CACNA1C NM_000719.7 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.05
• Publications: 15 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]

ITFG2-AS1 (HGNC:53128): (ITFG2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 12-2674806-T-C is Benign according to our data. Variant chr12-2674806-T-C is described in ClinVar as Benign. ClinVar VariationId is 671811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.4828+164T>C		intron_variant	Intron 39 of 46	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.4828+164T>C		intron_variant	Intron 39 of 46	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.4828+164T>C		intron_variant	Intron 39 of 46	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.4828+164T>C		intron_variant	Intron 39 of 46	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.5062+164T>C		intron_variant	Intron 41 of 49			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.4828+164T>C		intron_variant	Intron 39 of 47	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.4795+164T>C		intron_variant	Intron 38 of 46	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.4993+164T>C		intron_variant	Intron 40 of 47			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.4972+164T>C		intron_variant	Intron 41 of 48	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.4951+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.4828+164T>C		intron_variant	Intron 39 of 47	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.4828+164T>C		intron_variant	Intron 39 of 47	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.4918+164T>C		intron_variant	Intron 39 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.4918+164T>C		intron_variant	Intron 39 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.4918+164T>C		intron_variant	Intron 39 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.4918+164T>C		intron_variant	Intron 39 of 46			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.4912+164T>C		intron_variant	Intron 40 of 47	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.4903+164T>C		intron_variant	Intron 40 of 47	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.4888+164T>C		intron_variant	Intron 40 of 47	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.4885+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.4885+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.4885+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.4879+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.4870+164T>C		intron_variant	Intron 39 of 46			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.4852+164T>C		intron_variant	Intron 38 of 45	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.4852+164T>C		intron_variant	Intron 38 of 45	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.4846+164T>C		intron_variant	Intron 38 of 45	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.4828+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.4828+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.4828+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.4828+164T>C		intron_variant	Intron 39 of 46	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.4828+164T>C		intron_variant	Intron 39 of 46			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.4819+164T>C		intron_variant	Intron 39 of 46			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.4795+164T>C		intron_variant	Intron 38 of 45			ENSP00000507309.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108052 AN: 152016 Hom.: 40563 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.711 AC: 108094 AN: 152134 Hom.: 40573 Cov.: 33 AF XY: 0.714 AC XY: 53110 AN XY: 74386

African (AFR) AF: 0.450 AC: 18647 AN: 41458

American (AMR) AF: 0.741 AC: 11321 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2915 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3215 AN: 5154

South Asian (SAS) AF: 0.848 AC: 4088 AN: 4822

European-Finnish (FIN) AF: 0.859 AC: 9117 AN: 10618

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56382 AN: 68012

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.795 Hom.: 200571

Bravo AF: 0.689

Asia WGS AF: 0.724 AC: 2514 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Long QT syndrome Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: 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	-0.84
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-1.0
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: rs2302729; hg19: chr12-2783972;