rs833651

Variant names:

• chr3-62578213-G-A
• rs833651
• NM_003716.4:c.1577+6972C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-62578213-G-A
• chr3-62578213-G-C
• chr3-62578213-G-T

Variant summary

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

The NM_003716.4(CADPS):​c.1577+6972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 147,762 control chromosomes in the GnomAD database, including 62,476 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 0.92 (62476 hom., cov: 26)
• Consequence: CADPS NM_003716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADPS	NM_003716.4	MANE Select	c.1577+6972C>T		intron	N/A	NP_003707.2
	CADPS	NM_001438347.1		c.1577+6972C>T		intron	N/A	NP_001425276.1
	CADPS	NM_001438348.1		c.1577+6972C>T		intron	N/A	NP_001425277.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADPS	ENST00000383710.9	TSL:1 MANE Select	c.1577+6972C>T		intron	N/A	ENSP00000373215.4	Q9ULU8-1
	CADPS	ENST00000612439.4	TSL:1	c.1577+6972C>T		intron	N/A	ENSP00000484365.1	F1T0E5
	CADPS	ENST00000283269.13	TSL:1	c.1577+6972C>T		intron	N/A	ENSP00000283269.9	Q9ULU8-3

Frequencies

GnomAD3 genomes AF: 0.918 AC: 135629 AN: 147698 Hom.: 62446 Cov.: 26

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.918 AC: 135693 AN: 147762 Hom.: 62476 Cov.: 26 AF XY: 0.920 AC XY: 65971 AN XY: 71676

African (AFR) AF: 0.848 AC: 34111 AN: 40212

American (AMR) AF: 0.945 AC: 14105 AN: 14928

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3376 AN: 3466

East Asian (EAS) AF: 0.992 AC: 5014 AN: 5054

South Asian (SAS) AF: 0.948 AC: 4485 AN: 4732

European-Finnish (FIN) AF: 0.964 AC: 8486 AN: 8806

Middle Eastern (MID) AF: 0.907 AC: 263 AN: 290

European-Non Finnish (NFE) AF: 0.938 AC: 63099 AN: 67290

Other (OTH) AF: 0.924 AC: 1920 AN: 2078

Alfa AF: 0.935 Hom.: 87397

Bravo AF: 0.912

Asia WGS AF: 0.938 AC: 3242 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.18
PhyloP100		-0.15
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: rs833651; hg19: chr3-62563888;