Variant 7-122320353-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017954.11(CADPS2):c.3718-15A>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,574,906 control chromosomes in the GnomAD database, including 111,280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10155 hom., cov: 33)

Exomes 𝑓: 0.37 ( 101125 hom. )

Consequence

CADPS2
NM_017954.11 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.169

Variant links:

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]

CADPS2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 7-122320353-T-G is Benign according to our data. Variant chr7-122320353-T-G is described in ClinVar as [Benign]. Clinvar id is 1283565.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADPS2	NM_017954.11 linkuse as main transcript	c.3718-15A>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000449022.7	NP_060424.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADPS2	ENST00000449022.7 linkuse as main transcript	c.3718-15A>C		splice_polypyrimidine_tract_variant, intron_variant		5	NM_017954.11	ENSP00000398481		Q86UW7-1

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54963

AN:

151966

Hom.:

10156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.386

GnomAD3 exomes

AF:

0.392

AC:

88943

AN:

227126

Hom.:

17704

AF XY:

0.393

AC XY:

48611

AN XY:

123568

show subpopulations

Gnomad AFR exome

AF:

0.276

Gnomad AMR exome

AF:

0.426

Gnomad ASJ exome

AF:

0.434

Gnomad EAS exome

AF:

0.462

Gnomad SAS exome

AF:

0.399

Gnomad FIN exome

AF:

0.402

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.392

GnomAD4 exome

AF:

0.375

AC:

533162

AN:

1422822

Hom.:

101125

Cov.:

AF XY:

0.376

AC XY:

265636

AN XY:

706154

show subpopulations

Gnomad4 AFR exome

AF:

0.273

Gnomad4 AMR exome

AF:

0.425

Gnomad4 ASJ exome

AF:

0.434

Gnomad4 EAS exome

AF:

0.434

Gnomad4 SAS exome

AF:

0.399

Gnomad4 FIN exome

AF:

0.396

Gnomad4 NFE exome

AF:

0.369

Gnomad4 OTH exome

AF:

0.385

GnomAD4 genome

AF:

0.362

AC:

54981

AN:

152084

Hom.:

10155

Cov.:

AF XY:

0.365

AC XY:

27128

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.410

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.466

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.377

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.342

Hom.:

3229

Bravo

AF:

0.361

Asia WGS

AF:

0.389

AC:

1355

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 09, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.3

DANN

Benign

0.39

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over