rs1006737

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000719(CACNA1C):c.477+115699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151920 control chromosomes in the gnomAD Genomes database, including 10263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

Frequency

Genomes: 𝑓 0.35 ( 10263 hom., cov: 32)

Consequence

CACNA1C
NM_000719 intron

Scores

Clinical Significance

Uncertain risk allele no assertion criteria provided O:1

Conservation

PhyloP100: 0.248

Links

CACNA1C (HGNC:1390):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1C	NM_000719.7 linkuse as main transcript	c.477+115699G>A		intron_variant		ENST00000399655.6
CACNA1C	NM_001167623.2 linkuse as main transcript	c.477+115699G>A		intron_variant		ENST00000399603.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1C	ENST00000399603.6 linkuse as main transcript	c.477+115699G>A		intron_variant		5	NM_001167623.2		Q13936-37
CACNA1C	ENST00000399655.6 linkuse as main transcript	c.477+115699G>A		intron_variant		1	NM_000719.7		Q13936-12

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53833

AN:

151920

Hom.:

10263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.0516

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.328

Alfa

AF:

0.320

Hom.:

11497

Bravo

AF:

0.353

Asia WGS

AF:

0.150

AC:

527

AN:

3478

ClinVar

Significance: Uncertain risk allele

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Post-traumatic stress disorder

Other:1

Uncertain risk allele, no assertion criteria provided

research

Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

Cadd

Benign

4.2

Dann

Benign

0.63

Splicing

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over