rs304172

Variant names:

• chr3-62796793-G-A
• rs304172
• NM_003716.4:c.442-30809C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-62796793-G-A
• chr3-62796793-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.442-30809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,112 control chromosomes in the GnomAD database, including 646 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 0.079 (646 hom., cov: 33)
• Consequence: CADPS NM_003716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADPS	NM_003716.4	c.442-30809C>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.442-30809C>T		intron_variant	Intron 1 of 29	1	NM_003716.4	ENSP00000373215.4

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11924 AN: 151992 Hom.: 640 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.0934

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0786 AC: 11954 AN: 152112 Hom.: 646 Cov.: 33 AF XY: 0.0791 AC XY: 5880 AN XY: 74352

African (AFR) AF: 0.156 AC: 6466 AN: 41484

American (AMR) AF: 0.0456 AC: 696 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0393 AC: 136 AN: 3464

East Asian (EAS) AF: 0.0934 AC: 483 AN: 5172

South Asian (SAS) AF: 0.0637 AC: 307 AN: 4822

European-Finnish (FIN) AF: 0.0383 AC: 406 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3279 AN: 68002

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0618 Hom.: 1104

Bravo AF: 0.0836

Asia WGS AF: 0.0900 AC: 313 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.76
PhyloP100		0.17
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: rs304172; hg19: chr3-62782468;