7-122658652-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017954.11(CADPS2):​c.786+4585T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.989 in 152,252 control chromosomes in the GnomAD database, including 74,493 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 0.99 ( 74493 hom., cov: 31)

Consequence

CADPS2
NM_017954.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CADPS2NM_017954.11 linkuse as main transcriptc.786+4585T>C intron_variant ENST00000449022.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CADPS2ENST00000449022.7 linkuse as main transcriptc.786+4585T>C intron_variant 5 NM_017954.11 Q86UW7-1
CADPS2ENST00000412584.6 linkuse as main transcriptc.786+4585T>C intron_variant 1 P1Q86UW7-2
CADPS2ENST00000313070.11 linkuse as main transcriptc.468+4585T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.989
AC:
150472
AN:
152132
Hom.:
74434
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.964
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.997
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
0.978
Gnomad SAS
AF:
0.999
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.994
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.989
AC:
150591
AN:
152252
Hom.:
74493
Cov.:
31
AF XY:
0.989
AC XY:
73666
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.965
Gnomad4 AMR
AF:
0.997
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
0.978
Gnomad4 SAS
AF:
0.999
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
0.994
Alfa
AF:
0.994
Hom.:
8568
Bravo
AF:
0.987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.87
DANN
Benign
0.36

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.

Other links and lift over

dbSNP: rs2192022; hg19: chr7-122298706; API