rs304230

Variant names:

• chr3-62815398-G-A
• rs304230
• NM_003716.4:c.442-49414C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-62815398-G-A
• chr3-62815398-G-C

Variant summary

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

The NM_003716.4(CADPS):​c.442-49414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,450 control chromosomes in the GnomAD database, including 31,248 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 0.62 (31248 hom., cov: 28)
• Consequence: CADPS NM_003716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADPS	NM_003716.4	c.442-49414C>T		intron_variant	Intron 1 of 29	ENST00000383710.9	NP_003707.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADPS	ENST00000383710.9	c.442-49414C>T		intron_variant	Intron 1 of 29	1	NM_003716.4	ENSP00000373215.4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94462 AN: 151332 Hom.: 31254 Cov.: 28

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.624 AC: 94475 AN: 151450 Hom.: 31248 Cov.: 28 AF XY: 0.630 AC XY: 46648 AN XY: 73998

African (AFR) AF: 0.390 AC: 16094 AN: 41254

American (AMR) AF: 0.658 AC: 9988 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2510 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4521 AN: 5102

South Asian (SAS) AF: 0.790 AC: 3786 AN: 4790

European-Finnish (FIN) AF: 0.712 AC: 7476 AN: 10506

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47853 AN: 67824

Other (OTH) AF: 0.659 AC: 1390 AN: 2110

Alfa AF: 0.672 Hom.: 53819

Bravo AF: 0.608

Asia WGS AF: 0.769 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		0.42
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: rs304230; hg19: chr3-62801073;