chr2-17578901-A-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.31

Publications

2 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VSNL1NM_003385.5 linkc.-5-13169A>G intron_variant Intron 1 of 3 ENST00000295156.9 NP_003376.2 P62760

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VSNL1ENST00000295156.9 linkc.-5-13169A>G intron_variant Intron 1 of 3 1 NM_003385.5 ENSP00000295156.4 P62760
VSNL1ENST00000404666.6 linkc.-5-13169A>G intron_variant Intron 1 of 3 3 ENSP00000384014.1 P62760

Frequencies

GnomAD3 genomes
AF:
0.277
AC:
42163
AN:
151990
Hom.:
6591
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.189
Gnomad AMI
AF:
0.240
Gnomad AMR
AF:
0.236
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.0139
Gnomad SAS
AF:
0.112
Gnomad FIN
AF:
0.319
Gnomad MID
AF:
0.359
Gnomad NFE
AF:
0.361
Gnomad OTH
AF:
0.293
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.277
AC:
42166
AN:
152108
Hom.:
6591
Cov.:
32
AF XY:
0.270
AC XY:
20056
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.189
AC:
7833
AN:
41516
American (AMR)
AF:
0.236
AC:
3602
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.361
AC:
1251
AN:
3468
East Asian (EAS)
AF:
0.0137
AC:
71
AN:
5174
South Asian (SAS)
AF:
0.113
AC:
543
AN:
4820
European-Finnish (FIN)
AF:
0.319
AC:
3366
AN:
10566
Middle Eastern (MID)
AF:
0.366
AC:
106
AN:
290
European-Non Finnish (NFE)
AF:
0.361
AC:
24562
AN:
67966
Other (OTH)
AF:
0.290
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:
0.327
Hom.:
6886
Bravo
AF:
0.266
Asia WGS
AF:
0.0800
AC:
279
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
8.5
DANN
Benign
0.62
PhyloP100
2.3
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.54
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.54
Position offset: -5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12470654; hg19: chr2-17760168; API