rs798693

chr7-122353404-A-Gchr7-122353404-A-T

Variant summary

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

The NM_017954.11(CADPS2):c.3504+7384T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 151,918 control chromosomes in the GnomAD database, including 47,275 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 0.78 (47275 hom., cov: 29)
• Consequence: CADPS2 NM_017954.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

Genes affected

CADPS2 (HGNC:16018): (calcium dependent secretion activator 2) This gene encodes a member of the calcium-dependent activator of secretion (CAPS) protein family, which are calcium binding proteins that regulate the exocytosis of synaptic and dense-core vesicles in neurons and neuroendocrine cells. Mutations in this gene may contribute to autism susceptibility. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2009]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADPS2	NM_017954.11	c.3504+7384T>C		intron_variant		ENST00000449022.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADPS2	ENST00000449022.7	c.3504+7384T>C		intron_variant		5	NM_017954.11
	ENST00000630777.2	n.75-925A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119048 AN: 151800 Hom.: 47221 Cov.: 29

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.784 AC: 119162 AN: 151918 Hom.: 47275 Cov.: 29 AF XY: 0.782 AC XY: 58079 AN XY: 74250

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.755

Alfa AF: 0.781 Hom.: 5458

Bravo AF: 0.779

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	7.7
Dann	Benign	0.44

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: rs798693; hg19: chr7-121993458;