chr3-53813035-G-A

Variant names:

• chr3-53813035-G-A
• rs893363
• NM_000720.4:c.*1629G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000720.4(CACNA1D):​c.*1629G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,888 control chromosomes in the GnomAD database, including 25,373 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 0.55 (25369 hom., cov: 32)
  • Exomes 𝑓: 0.67 (4 hom.)
• Consequence: CACNA1D NM_000720.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 21 publications found

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]

CHDH (HGNC:24288): (choline dehydrogenase) The protein encoded by this gene is a choline dehydrogenase that localizes to the mitochondrion. Variations in this gene can affect susceptibility to choline deficiency. A few transcript variants have been found for this gene, but the full-length nature of only one has been characterized to date. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000720.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA1D	NM_000720.4	MANE Plus Clinical	c.*1629G>A		3_prime_UTR	Exon 49 of 49	NP_000711.1
	CACNA1D	NM_001128840.3	MANE Select	c.*1629G>A		3_prime_UTR	Exon 48 of 48	NP_001122312.1
	CHDH	NM_018397.5	MANE Select	c.*4742C>T		3_prime_UTR	Exon 9 of 9	NP_060867.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA1D	ENST00000288139.11	TSL:1 MANE Plus Clinical	c.*1629G>A		3_prime_UTR	Exon 49 of 49	ENSP00000288139.3
	CACNA1D	ENST00000350061.11	TSL:1 MANE Select	c.*1629G>A		3_prime_UTR	Exon 48 of 48	ENSP00000288133.5
	CHDH	ENST00000315251.11	TSL:1 MANE Select	c.*4742C>T		3_prime_UTR	Exon 9 of 9	ENSP00000319851.5

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84046 AN: 151752 Hom.: 25350 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.601

GnomAD4 exome AF: 0.667 AC: 12 AN: 18 Hom.: 4 Cov.: 0 AF XY: 0.625 AC XY: 10 AN XY: 16

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.688 AC: 11 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.554 AC: 84115 AN: 151870 Hom.: 25369 Cov.: 32 AF XY: 0.561 AC XY: 41666 AN XY: 74214

African (AFR) AF: 0.309 AC: 12790 AN: 41398

American (AMR) AF: 0.683 AC: 10437 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4973 AN: 5172

South Asian (SAS) AF: 0.740 AC: 3555 AN: 4802

European-Finnish (FIN) AF: 0.584 AC: 6139 AN: 10520

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42051 AN: 67924

Other (OTH) AF: 0.606 AC: 1277 AN: 2108

Alfa AF: 0.606 Hom.: 26270

Bravo AF: 0.549

Asia WGS AF: 0.833 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.24
DANN	Benign	0.69
PhyloP100		0.19
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
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: rs893363; hg19: chr3-53847062; COSMIC: COSV55449332; COSMIC: COSV55449332;