7-122417181-C-T

Variant names:

• chr7-122417181-C-T
• rs6947805
• NM_017954.11:c.2477-1017G>A

Variant summary

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

The NM_017954.11(CADPS2):​c.2477-1017G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,094 control chromosomes in the GnomAD database, including 1,717 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 (1717 hom., cov: 32)
• Consequence: CADPS2 NM_017954.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADPS2	NM_017954.11	c.2477-1017G>A		intron_variant	Intron 17 of 29	ENST00000449022.7	NP_060424.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADPS2	ENST00000449022.7	c.2477-1017G>A		intron_variant	Intron 17 of 29	5	NM_017954.11	ENSP00000398481.2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18411 AN: 151976 Hom.: 1707 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.121 AC: 18468 AN: 152094 Hom.: 1717 Cov.: 32 AF XY: 0.121 AC XY: 9033 AN XY: 74368

African (AFR) AF: 0.255 AC: 10584 AN: 41458

American (AMR) AF: 0.0753 AC: 1153 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.0385 AC: 199 AN: 5166

South Asian (SAS) AF: 0.0564 AC: 271 AN: 4808

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10578

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4382 AN: 67992

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0894 Hom.: 342

Bravo AF: 0.122

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.49
PhyloP100		-0.49
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: rs6947805; hg19: chr7-122057235;