7-122380329-A-C

Position:

• chr7-122380329-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017954.11(CADPS2):​c.3313-887T>G variant causes a intron change. The variant allele was found at a frequency of 0.118 in 152,152 control chromosomes in the GnomAD database, including 1,442 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 0.12 (1442 hom., cov: 32)
• Consequence: CADPS2 NM_017954.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.07

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADPS2	NM_017954.11	c.3313-887T>G		intron_variant		ENST00000449022.7	NP_060424.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADPS2	ENST00000449022.7	c.3313-887T>G		intron_variant		5	NM_017954.11	ENSP00000398481
	ENST00000630777.2	n.162+25913A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17938 AN: 152034 Hom.: 1443 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.118 AC: 17926 AN: 152152 Hom.: 1442 Cov.: 32 AF XY: 0.113 AC XY: 8387 AN XY: 74374

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.111

Alfa AF: 0.168 Hom.: 3433

Bravo AF: 0.113

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	19
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs7801807; hg19: chr7-122020383;