rs17205986

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196

Publications

3 publications found
Variant links:
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)

Genome browser will be placed here

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
VCANNM_004385.5 linkc.9736-7855T>G intron_variant Intron 12 of 14 ENST00000265077.8 NP_004376.2 P13611-1A0A024RAQ9Q59FG9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VCANENST00000265077.8 linkc.9736-7855T>G intron_variant Intron 12 of 14 1 NM_004385.5 ENSP00000265077.3 P13611-1

Frequencies

GnomAD3 genomes
AF:
0.0437
AC:
6655
AN:
152182
Hom.:
190
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0122
Gnomad AMI
AF:
0.0603
Gnomad AMR
AF:
0.0438
Gnomad ASJ
AF:
0.00950
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00951
Gnomad FIN
AF:
0.0639
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0673
Gnomad OTH
AF:
0.0430
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0437
AC:
6658
AN:
152298
Hom.:
191
Cov.:
32
AF XY:
0.0426
AC XY:
3170
AN XY:
74462
show subpopulations
African (AFR)
AF:
0.0122
AC:
506
AN:
41576
American (AMR)
AF:
0.0439
AC:
672
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.00950
AC:
33
AN:
3472
East Asian (EAS)
AF:
0.000386
AC:
2
AN:
5186
South Asian (SAS)
AF:
0.00931
AC:
45
AN:
4834
European-Finnish (FIN)
AF:
0.0639
AC:
678
AN:
10612
Middle Eastern (MID)
AF:
0.00685
AC:
2
AN:
292
European-Non Finnish (NFE)
AF:
0.0673
AC:
4575
AN:
67996
Other (OTH)
AF:
0.0425
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:
0.0600
Hom.:
39
Bravo
AF:
0.0393
Asia WGS
AF:
0.00606
AC:
21
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.7
DANN
Benign
0.57
PhyloP100
-0.20
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs17205986; hg19: chr5-82860380; API