chr15:42399483:A>G Detail (hg38) (CAPN3)

Information

Genome

Assembly Position
hg19 chr15:42,691,681-42,691,681 View the variant detail on this assembly version.
hg38 chr15:42,399,483-42,399,483

HGVS

Type Transcript Protein
RefSeq NM_000070.2:c.1194-9A>G
NM_173087.1:c.1050-9A>G
NM_024344.1:c.1194-9A>G
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 114240 OMIM
HGNC 1480 HGNC
Ensembl ENSG00000092529 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv52709883 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic muscular dystrophy, limb-girdle, autosomal recessive germline MGS000074
(TMGS000150) 		Kenjiro Kosaki
Nishino Ichizo		 Keio University
National Center of Neurology and Psychiatry
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2023-11-06 criteria provided, single submitter autosomal recessive limb-girdle muscular dystrophy type 2A germline unknown Detail
Pathogenic 2023-04-24 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2023-05-02 criteria provided, single submitter autosomal recessive limb-girdle muscular dystrophy germline Detail
Pathogenic 2023-10-20 criteria provided, single submitter Muscular dystrophy, limb-girdle, autosomal dominant 4 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.573 Limb-girdle muscular dystrophy type 2A NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000070.3(CAPN3):c.1194-9A>G AND Autosomal recessive limb-girdle muscular dystrophy type 2A ClinVar Detail
NM_000070.3(CAPN3):c.1194-9A>G AND not provided ClinVar Detail
NM_000070.3(CAPN3):c.1194-9A>G AND Autosomal recessive limb-girdle muscular dystrophy ClinVar Detail
NM_000070.3(CAPN3):c.1194-9A>G AND Muscular dystrophy, limb-girdle, autosomal dominant 4 ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs374665929 dbSNP
Genome
hg38
Position
chr15:42,399,483-42,399,483
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
229.12
Standard deviation of sample read depth (HGVD)
100.60
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
CAPN3
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))
rs374665929
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)
8652
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)
121392
Allele Counts in All Race (ExAC)
2
Heterozygous Counts in All Race (ExAC)
2
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.6475550283379465E-5
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