rs17411949
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022131.3(CLSTN2):c.233-22778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.045 in 152,222 control chromosomes in the GnomAD database, including 182 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 0.045 ( 182 hom., cov: 32)
Consequence
CLSTN2
NM_022131.3 intron
NM_022131.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.746
Publications
10 publications found
Genes affected
CLSTN2 (HGNC:17448): (calsyntenin 2) Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Predicted to be located in postsynaptic density. Predicted to be active in cell surface; glutamatergic synapse; and postsynaptic membrane. Predicted to be integral component of postsynaptic density 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 (SAS) allele frequency at 95% confidence interval = 0.0612 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0450 AC: 6840AN: 152106Hom.: 177 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6840
AN:
152106
Hom.:
Cov.:
32
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: 0.0450 AC: 6852AN: 152222Hom.: 182 Cov.: 32 AF XY: 0.0439 AC XY: 3265AN XY: 74410 show subpopulations
GnomAD4 genome
AF:
AC:
6852
AN:
152222
Hom.:
Cov.:
32
AF XY:
AC XY:
3265
AN XY:
74410
show subpopulations
African (AFR)
AF:
AC:
1543
AN:
41538
American (AMR)
AF:
AC:
684
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
122
AN:
3468
East Asian (EAS)
AF:
AC:
310
AN:
5176
South Asian (SAS)
AF:
AC:
324
AN:
4816
European-Finnish (FIN)
AF:
AC:
147
AN:
10604
Middle Eastern (MID)
AF:
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3537
AN:
68016
Other (OTH)
AF:
AC:
126
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
342
684
1026
1368
1710
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
78
156
234
312
390
<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:
316
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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