chr7:143320675:C>T Detail (hg38) (CLCN1)

Information

Genome

Assembly Position
hg19 chr7:143,017,768-143,017,768 View the variant detail on this assembly version.
hg38 chr7:143,320,675-143,320,675

HGVS

Type Transcript Protein
RefSeq NM_000083.2:c.313C>T NP_000074.2:p.Arg105Cys
NR_046453.1:c.313C>T
Ensemble ENST00000343257.7:c.313C>T ENST00000343257.7:p.Arg105Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 118425 OMIM
HGNC 2019 HGNC
Ensembl ENSG00000188037 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv31297628 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2022-10-31 criteria provided, single submitter Congenital myotonia, autosomal dominant form,Congenital myotonia, autosomal recessive form germline Detail
Uncertain significance 2022-10-31 criteria provided, single submitter Congenital myotonia, autosomal dominant form,Congenital myotonia, autosomal recessive form germline Detail
Conflicting interpretations of pathogenicity 2023-01-30 criteria provided, conflicting interpretations not provided germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Batten-Turner congenital myopathy germline Detail
Likely pathogenic 2022-11-15 no assertion criteria provided germline Detail
Uncertain significance 2024-03-01 criteria provided, single submitter Congenital myotonia, autosomal recessive form germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.321 Becker Generalized Myotonia NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND multiple conditions ClinVar Detail
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND multiple conditions ClinVar Detail
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND not provided ClinVar Detail
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND Batten-Turner congenital myopathy ClinVar Detail
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND Tip-toe gait ClinVar Detail
NM_000083.3(CLCN1):c.313C>T (p.Arg105Cys) AND Congenital myotonia, autosomal recessive form ClinVar 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
rs201509501 dbSNP
Genome
hg38
Position
chr7:143,320,675-143,320,675
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1133
Mean of sample read depth (HGVD)
31.29
Standard deviation of sample read depth (HGVD)
17.56
Number of reference allele (HGVD)
2262
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.00176522506619594
Gene Symbol (HGVD)
CLCN1
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))
rs201509501
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
20
East Asian Heterozygous Counts (ExAC)
20
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0023142791020597086
Chromosome Counts in All Race (ExAC)
121342
Allele Counts in All Race (ExAC)
34
Heterozygous Counts in All Race (ExAC)
34
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.801997659507837E-4
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