NM_017954.11:c.3388-2899C>T

Variant names:

• chr7-122363912-G-A
• rs9641684
• NM_017954.11:c.3388-2899C>T

Variant summary

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

The NM_017954.11(CADPS2):​c.3388-2899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,892 control chromosomes in the GnomAD database, including 9,924 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 0.36 (9924 hom., cov: 31)
• Consequence: CADPS2 NM_017954.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017954.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADPS2	NM_017954.11	MANE Select	c.3388-2899C>T		intron	N/A	NP_060424.9
	CADPS2	NM_001363389.2		c.3424-2899C>T		intron	N/A	NP_001350318.1
	CADPS2	NM_001363390.2		c.3409-2899C>T		intron	N/A	NP_001350319.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADPS2	ENST00000449022.7	TSL:5 MANE Select	c.3388-2899C>T		intron	N/A	ENSP00000398481.2
	CADPS2	ENST00000412584.6	TSL:1	c.3265-2899C>T		intron	N/A	ENSP00000400401.2
	CADPS2	ENST00000313070.11	TSL:5	c.3082-2899C>T		intron	N/A	ENSP00000325581.8

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54033 AN: 151774 Hom.: 9918 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.356 AC: 54086 AN: 151892 Hom.: 9924 Cov.: 31 AF XY: 0.361 AC XY: 26799 AN XY: 74214

African (AFR) AF: 0.355 AC: 14710 AN: 41402

American (AMR) AF: 0.397 AC: 6053 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1261 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2845 AN: 5136

South Asian (SAS) AF: 0.389 AC: 1870 AN: 4812

European-Finnish (FIN) AF: 0.362 AC: 3816 AN: 10556

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22461 AN: 67964

Other (OTH) AF: 0.354 AC: 746 AN: 2108

Alfa AF: 0.342 Hom.: 4721

Bravo AF: 0.356

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-1.2
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: rs9641684; hg19: chr7-122003966;