chr2-17578901-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PP3BA1
The NM_003385.5(VSNL1):c.-5-13169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,108 control chromosomes in the GnomAD database, including 6,591 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 0.28 ( 6591 hom., cov: 32)
Consequence
VSNL1
NM_003385.5 intron
NM_003385.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.31
Publications
2 publications found
Genes affected
VSNL1 (HGNC:12722): (visinin like 1) This gene is a member of the visinin/recoverin subfamily of neuronal calcium sensor proteins. The encoded protein is strongly expressed in granule cells of the cerebellum where it associates with membranes in a calcium-dependent manner and modulates intracellular signaling pathways of the central nervous system by directly or indirectly regulating the activity of adenylyl cyclase. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
PP3
Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.277 AC: 42163AN: 151990Hom.: 6591 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
42163
AN:
151990
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: 0.277 AC: 42166AN: 152108Hom.: 6591 Cov.: 32 AF XY: 0.270 AC XY: 20056AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
42166
AN:
152108
Hom.:
Cov.:
32
AF XY:
AC XY:
20056
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
7833
AN:
41516
American (AMR)
AF:
AC:
3602
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1251
AN:
3468
East Asian (EAS)
AF:
AC:
71
AN:
5174
South Asian (SAS)
AF:
AC:
543
AN:
4820
European-Finnish (FIN)
AF:
AC:
3366
AN:
10566
Middle Eastern (MID)
AF:
AC:
106
AN:
290
European-Non Finnish (NFE)
AF:
AC:
24562
AN:
67966
Other (OTH)
AF:
AC:
613
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1496
2993
4489
5986
7482
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
420
840
1260
1680
2100
<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:
279
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
DS_DG_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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