12-2653882-C-T

Position:

chr12-2653882-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_000719.7(CACNA1C):c.4122C>T(p.Tyr1374Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,878 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: 𝑓 0.00018 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

CACNA1C
NM_000719.7 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.238

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 12-2653882-C-T is Benign according to our data. Variant chr12-2653882-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 381370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.238 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000184 (28/152304) while in subpopulation AFR AF= 0.000505 (21/41560). AF 95% confidence interval is 0.000338. There are 0 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 28 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	ENST00000399655.6	NP_000710.5	Q13936-12
CACNA1C	NM_001167623.2 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	ENST00000399603.6	NP_001161095.1	Q13936-37

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CACNA1C	ENST00000399603.6 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	5	NM_001167623.2	ENSP00000382512.1	Q13936-37
CACNA1C	ENST00000399655.6 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1	NM_000719.7	ENSP00000382563.1	Q13936-12
CACNA1C	ENST00000682544.1 link	c.4356C>T	p.Tyr1452Tyr	synonymous_variant	35/50			ENSP00000507184.1	A0A804HIR0
CACNA1C	ENST00000406454.8 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/48	5		ENSP00000385896.3	F5GY28
CACNA1C	ENST00000399634.6 link	c.4089C>T	p.Tyr1363Tyr	synonymous_variant	32/47	5		ENSP00000382542.2	E9PDI6
CACNA1C	ENST00000683824.1 link	c.4287C>T	p.Tyr1429Tyr	synonymous_variant	34/48			ENSP00000507867.1	A0A804HKC4
CACNA1C	ENST00000347598.9 link	c.4266C>T	p.Tyr1422Tyr	synonymous_variant	35/49	1		ENSP00000266376.6	Q13936-11
CACNA1C	ENST00000344100.7 link	c.4188C>T	p.Tyr1396Tyr	synonymous_variant	33/47	1		ENSP00000341092.3	Q13936-14
CACNA1C	ENST00000327702.12 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/48	1		ENSP00000329877.7	A0A0A0MR67
CACNA1C	ENST00000399617.6 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/48	5		ENSP00000382526.1	A0A0A0MSA1
CACNA1C	ENST00000682462.1 link	c.4212C>T	p.Tyr1404Tyr	synonymous_variant	33/47			ENSP00000507105.1	A0A804HIJ8
CACNA1C	ENST00000683781.1 link	c.4212C>T	p.Tyr1404Tyr	synonymous_variant	33/47			ENSP00000507434.1	A0A804HJB6
CACNA1C	ENST00000683840.1 link	c.4212C>T	p.Tyr1404Tyr	synonymous_variant	33/47			ENSP00000507612.1	A0A804HJR1
CACNA1C	ENST00000683956.1 link	c.4212C>T	p.Tyr1404Tyr	synonymous_variant	33/47			ENSP00000506882.1	A0A804HI37
CACNA1C	ENST00000399638.5 link	c.4206C>T	p.Tyr1402Tyr	synonymous_variant	34/48	1		ENSP00000382547.1	Q13936-31
CACNA1C	ENST00000335762.10 link	c.4197C>T	p.Tyr1399Tyr	synonymous_variant	34/48	5		ENSP00000336982.5	F5H522
CACNA1C	ENST00000399606.5 link	c.4182C>T	p.Tyr1394Tyr	synonymous_variant	34/48	1		ENSP00000382515.1	Q13936-30
CACNA1C	ENST00000399621.5 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382530.1	Q13936-24
CACNA1C	ENST00000399637.5 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382546.1	Q13936-27
CACNA1C	ENST00000402845.7 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000385724.3	Q13936-13
CACNA1C	ENST00000399629.5 link	c.4173C>T	p.Tyr1391Tyr	synonymous_variant	33/47	1		ENSP00000382537.1	Q13936-32
CACNA1C	ENST00000682336.1 link	c.4164C>T	p.Tyr1388Tyr	synonymous_variant	33/47			ENSP00000507898.1	A0A804HKE9
CACNA1C	ENST00000399591.5 link	c.4089C>T	p.Tyr1363Tyr	synonymous_variant	32/46	1		ENSP00000382500.1	Q13936-29
CACNA1C	ENST00000399595.5 link	c.4089C>T	p.Tyr1363Tyr	synonymous_variant	32/46	1		ENSP00000382504.1	Q13936-25
CACNA1C	ENST00000399649.5 link	c.4083C>T	p.Tyr1361Tyr	synonymous_variant	32/46	1		ENSP00000382557.1	Q13936-15
CACNA1C	ENST00000399597.5 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382506.1	Q13936-22
CACNA1C	ENST00000399601.5 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382510.1	Q13936-20
CACNA1C	ENST00000399641.6 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382549.1	Q13936-23
CACNA1C	ENST00000399644.5 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47	1		ENSP00000382552.1	Q13936-21
CACNA1C	ENST00000682835.1 link	c.4122C>T	p.Tyr1374Tyr	synonymous_variant	33/47			ENSP00000507282.1	A0A804HIZ0
CACNA1C	ENST00000683482.1 link	c.4113C>T	p.Tyr1371Tyr	synonymous_variant	33/47			ENSP00000507169.1	Q13936-35
CACNA1C	ENST00000682686.1 link	c.4089C>T	p.Tyr1363Tyr	synonymous_variant	32/46			ENSP00000507309.1	Q13936-19

Frequencies

GnomAD3 genomes

AF:

0.000177

AC:

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.0000603

AC:

AN:

248802

Hom.:

AF XY:

0.0000370

AC XY:

AN XY:

135016

show subpopulations

Gnomad AFR exome

AF:

0.000905

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000165

GnomAD4 exome

AF:

0.0000308

AC:

AN:

1461574

Hom.:

Cov.:

AF XY:

0.0000261

AC XY:

AN XY:

727066

show subpopulations

Gnomad4 AFR exome

AF:

0.000568

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000144

Gnomad4 OTH exome

AF:

0.000116

GnomAD4 genome

AF:

0.000184

AC:

AN:

152304

Hom.:

Cov.:

AF XY:

0.000161

AC XY:

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000115

Hom.:

Bravo

AF:

0.000147

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 29, 2020

- -

Long QT syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 14, 2024

- -

Cardiovascular phenotype

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 19, 2017

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

7.9

DANN

Benign

0.50

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over