rs136855

Positions:

• chr22-39665678-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021096.4(CACNA1I):​c.3978+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,594,494 control chromosomes in the GnomAD database, including 43,491 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 0.26 (5619 hom., cov: 32)
  • Exomes 𝑓: 0.22 (37872 hom.)
• Consequence: CACNA1I NM_021096.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

CACNA1I (HGNC:1396): (calcium voltage-gated channel subunit alpha1 I) This gene encodes the pore-forming alpha subunit of a voltage gated calcium channel. The encoded protein is a member of a subfamily of calcium channels referred to as is a low voltage-activated, T-type, calcium channel. The channel encoded by this protein is characterized by a slower activation and inactivation compared to other T-type calcium channels. This protein may be involved in calcium signaling in neurons. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1I	NM_021096.4	c.3978+54A>G		intron_variant		ENST00000402142.4
CACNA1I	NM_001003406.2	c.3873+54A>G		intron_variant
CACNA1I	XM_017029035.3	c.2124+54A>G		intron_variant
CACNA1I	XM_017029036.2	c.2124+54A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1I	ENST00000402142.4	c.3978+54A>G		intron_variant		1	NM_021096.4	A2
CACNA1I	ENST00000401624.5	c.3978+54A>G		intron_variant		1		P4
CACNA1I	ENST00000404898.5	c.3873+54A>G		intron_variant		1		A2
CACNA1I	ENST00000407673.5	c.3873+54A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39457 AN: 151858 Hom.: 5617 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.222 AC: 320848 AN: 1442518 Hom.: 37872 Cov.: 30 AF XY: 0.220 AC XY: 157487 AN XY: 714954

Gnomad4 AFR exome AF: 0.365

Gnomad4 AMR exome AF: 0.290

Gnomad4 ASJ exome AF: 0.289

Gnomad4 EAS exome AF: 0.0437

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.232

Gnomad4 NFE exome AF: 0.226

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.260 AC: 39492 AN: 151976 Hom.: 5619 Cov.: 32 AF XY: 0.253 AC XY: 18784 AN XY: 74264

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.286

Alfa AF: 0.250 Hom.: 5995

Bravo AF: 0.272

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs136855; hg19: chr22-40061683; COSMIC: COSV60803532;