rs9932538
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016524.4(SYT17):c.951+13100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,226 control chromosomes in the GnomAD database, including 2,140 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 0.16 ( 2140 hom., cov: 33)
Consequence
SYT17
NM_016524.4 intron
NM_016524.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.314
Publications
4 publications found
Genes affected
SYT17 (HGNC:24119): (synaptotagmin 17) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Predicted to be located in trans-Golgi network. Predicted to be active in exocytic vesicle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24730AN: 152108Hom.: 2136 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
24730
AN:
152108
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.163 AC: 24753AN: 152226Hom.: 2140 Cov.: 33 AF XY: 0.160 AC XY: 11880AN XY: 74438 show subpopulations
GnomAD4 genome
AF:
AC:
24753
AN:
152226
Hom.:
Cov.:
33
AF XY:
AC XY:
11880
AN XY:
74438
show subpopulations
African (AFR)
AF:
AC:
8405
AN:
41516
American (AMR)
AF:
AC:
2386
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
725
AN:
3464
East Asian (EAS)
AF:
AC:
97
AN:
5190
South Asian (SAS)
AF:
AC:
844
AN:
4830
European-Finnish (FIN)
AF:
AC:
1142
AN:
10602
Middle Eastern (MID)
AF:
AC:
45
AN:
294
European-Non Finnish (NFE)
AF:
AC:
10572
AN:
68004
Other (OTH)
AF:
AC:
349
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1095
2190
3284
4379
5474
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
268
536
804
1072
1340
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
430
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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