chr3-53798876-T-G

Position:

• chr3-53798876-T-G

Variant summary

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

The ENST00000350061.11(CACNA1D):​c.4924-1373T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,022 control chromosomes in the GnomAD database, including 22,523 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 0.51 (22523 hom., cov: 32)
• Consequence: CACNA1D ENST00000350061.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

CACNA1D (HGNC:1391): (calcium voltage-gated channel subunit alpha1 D) Voltage-dependent calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, namely alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1D subunit. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1D	NM_000720.4	c.4984-1373T>G		intron_variant		ENST00000288139.11	NP_000711.1
CACNA1D	NM_001128840.3	c.4924-1373T>G		intron_variant		ENST00000350061.11	NP_001122312.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1D	ENST00000288139.11	c.4984-1373T>G		intron_variant		1	NM_000720.4	ENSP00000288139	P2
CACNA1D	ENST00000350061.11	c.4924-1373T>G		intron_variant		1	NM_001128840.3	ENSP00000288133

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77557 AN: 151904 Hom.: 22470 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.511 AC: 77674 AN: 152022 Hom.: 22523 Cov.: 32 AF XY: 0.503 AC XY: 37386 AN XY: 74326

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.475

Alfa AF: 0.384 Hom.: 5541

Bravo AF: 0.540

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.76

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: rs3774609; hg19: chr3-53832903;