rs17205986
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004385.5(VCAN):c.9736-7855T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,298 control chromosomes in the GnomAD database, including 191 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 0.044 ( 191 hom., cov: 32)
Consequence
VCAN
NM_004385.5 intron
NM_004385.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.196
Publications
3 publications found
Genes affected
VCAN (HGNC:2464): (versican) This gene is a member of the aggrecan/versican proteoglycan family. The protein encoded is a large chondroitin sulfate proteoglycan and is a major component of the extracellular matrix. This protein is involved in cell adhesion, proliferation, proliferation, migration and angiogenesis and plays a central role in tissue morphogenesis and maintenance. Mutations in this gene are the cause of Wagner syndrome type 1. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
VCAN-AS1 (HGNC:40163): (VCAN antisense RNA 1)
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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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.9736-7855T>G | intron_variant | Intron 12 of 14 | ENST00000265077.8 | NP_004376.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0437 AC: 6655AN: 152182Hom.: 190 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6655
AN:
152182
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: 0.0437 AC: 6658AN: 152298Hom.: 191 Cov.: 32 AF XY: 0.0426 AC XY: 3170AN XY: 74462 show subpopulations
GnomAD4 genome
AF:
AC:
6658
AN:
152298
Hom.:
Cov.:
32
AF XY:
AC XY:
3170
AN XY:
74462
show subpopulations
African (AFR)
AF:
AC:
506
AN:
41576
American (AMR)
AF:
AC:
672
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
33
AN:
3472
East Asian (EAS)
AF:
AC:
2
AN:
5186
South Asian (SAS)
AF:
AC:
45
AN:
4834
European-Finnish (FIN)
AF:
AC:
678
AN:
10612
Middle Eastern (MID)
AF:
AC:
2
AN:
292
European-Non Finnish (NFE)
AF:
AC:
4575
AN:
67996
Other (OTH)
AF:
AC:
90
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
330
660
991
1321
1651
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
72
144
216
288
360
<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:
21
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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