NM_004385.5:c.1042+2499A>G
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.1042+2499A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,146 control chromosomes in the GnomAD database, including 10,589 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 0.37 ( 10589 hom., cov: 33)
Consequence
VCAN
NM_004385.5 intron
NM_004385.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.68
Publications
7 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 Gene-Disease associations (from GenCC):
- Wagner diseaseInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
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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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.1042+2499A>G | intron_variant | Intron 6 of 14 | ENST00000265077.8 | NP_004376.2 | ||
VCAN | NM_001164097.2 | c.1042+2499A>G | intron_variant | Intron 6 of 13 | NP_001157569.1 | |||
VCAN | NM_001164098.2 | c.1042+2499A>G | intron_variant | Intron 6 of 13 | NP_001157570.1 | |||
VCAN | NM_001126336.3 | c.1042+2499A>G | intron_variant | Intron 6 of 12 | NP_001119808.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.366 AC: 55709AN: 152028Hom.: 10585 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
55709
AN:
152028
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: 0.366 AC: 55742AN: 152146Hom.: 10589 Cov.: 33 AF XY: 0.370 AC XY: 27526AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
55742
AN:
152146
Hom.:
Cov.:
33
AF XY:
AC XY:
27526
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
16087
AN:
41504
American (AMR)
AF:
AC:
6868
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
1515
AN:
3464
East Asian (EAS)
AF:
AC:
2964
AN:
5160
South Asian (SAS)
AF:
AC:
2051
AN:
4818
European-Finnish (FIN)
AF:
AC:
3315
AN:
10584
Middle Eastern (MID)
AF:
AC:
135
AN:
292
European-Non Finnish (NFE)
AF:
AC:
21636
AN:
68002
Other (OTH)
AF:
AC:
831
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1800
3600
5401
7201
9001
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1704
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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