chr7-122353404-A-G

Variant names:

• chr7-122353404-A-G
• rs798693
• NM_017954.11:c.3504+7384T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ENSG00000240499 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CADPS2	NM_017954.11	c.3504+7384T>C		intron_variant	Intron 27 of 29	ENST00000449022.7	NP_060424.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADPS2	ENST00000449022.7	c.3504+7384T>C		intron_variant	Intron 27 of 29	5	NM_017954.11	ENSP00000398481.2

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

African (AFR) AF: 0.887 AC: 36779 AN: 41462

American (AMR) AF: 0.707 AC: 10786 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2406 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3158 AN: 5140

South Asian (SAS) AF: 0.706 AC: 3382 AN: 4792

European-Finnish (FIN) AF: 0.784 AC: 8283 AN: 10564

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51838 AN: 67920

Other (OTH) AF: 0.755 AC: 1589 AN: 2104

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
PhyloP100		0.83
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: rs798693; hg19: chr7-121993458;