rs1231831

chr3-62615691-T-C

Variant summary

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

The NM_003716.4(CADPS):c.1326-22943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,920 control chromosomes in the GnomAD database, including 7,770 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 0.30 (7770 hom., cov: 32)
• Consequence: CADPS NM_003716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

CADPS (HGNC:1426): (calcium dependent secretion activator) This gene encodes a novel neural/endocrine-specific cytosolic and peripheral membrane protein required for the Ca2+-regulated exocytosis of secretory vesicles. The protein acts at a stage in exocytosis that follows ATP-dependent priming, which involves the essential synthesis of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). Alternative splicing has been observed at this locus and three variants, encoding distinct isoforms, are described. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADPS	NM_003716.4	c.1326-22943A>G		intron_variant		ENST00000383710.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADPS	ENST00000383710.9	c.1326-22943A>G		intron_variant		1	NM_003716.4	P2
CADPS	ENST00000283269.13	c.1326-22943A>G		intron_variant		1		A2
CADPS	ENST00000357948.7	c.1326-22943A>G		intron_variant		1
CADPS	ENST00000612439.4	c.1326-22943A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45951 AN: 151802 Hom.: 7767 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.303 AC: 45970 AN: 151920 Hom.: 7770 Cov.: 32 AF XY: 0.298 AC XY: 22143 AN XY: 74220

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.301

Alfa AF: 0.355 Hom.: 9547

Bravo AF: 0.297

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.051
Dann	Benign	0.31

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: rs1231831; hg19: chr3-62601366;