chr12:47974090:G>A Detail (hg38) (COL2A1)

Information

Genome

Assembly Position
hg19 chr12:48,367,873-48,367,873 View the variant detail on this assembly version.
hg38 chr12:47,974,090-47,974,090

HGVS

Type Transcript Protein
RefSeq NM_001844.4:c.4316C>T NP_001835.3:p.Thr1439Met
NM_033150.2:c.4109C>T NP_149162.2:p.Thr1370Met
Ensemble ENST00000380518.8:c.4316C>T ENST00000380518.8:p.Thr1439Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 120140 OMIM
HGNC 2200 HGNC
Ensembl ENSG00000139219 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv45753054 TogoVar
COSMIC COSM4042156 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2019-01-01 criteria provided, single submitter spondyloepiphyseal dysplasia congenita germline unknown Detail
Likely pathogenic 2014-09-15 criteria provided, single submitter spondyloperipheral dysplasia germline Detail
Uncertain significance 2024-01-18 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.125 spondyloepiphyseal dysplasia NA CLINVAR Detail
0.361 Spondyloperipheral dysplasia short ulna NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001844.5(COL2A1):c.4316C>T (p.Thr1439Met) AND Spondyloepiphyseal dysplasia congenita ClinVar Detail
NM_001844.5(COL2A1):c.4316C>T (p.Thr1439Met) AND Spondyloperipheral dysplasia ClinVar Detail
NM_001844.5(COL2A1):c.4316C>T (p.Thr1439Met) AND not provided ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs121912886 dbSNP
Genome
hg38
Position
chr12:47,974,090-47,974,090
Variant Type
snv
Reference Allele
G
Alternative Allele
A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs121912886
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
121340
Allele Counts in All Race (ExAC)
7
Heterozygous Counts in All Race (ExAC)
7
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
5.768913795945278E-5
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