chr2:167129390:A> Detail (hg19) (SCN9A, SCN1A-AS1)

Information

Genome

Assembly Position
hg19 chr2:167,129,390-167,129,390
hg38 chr2:166,272,880-166,272,880 

HGVS

Type Transcript Protein
RefSeq NM_002977.3:c.2842-5delT
Ensemble ENST00000303354.11:c.2875-5delT
ENST00000409672.5:c.2842-5delT
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.007

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603415 OMIM
HGNC 10597 HGNC
Ensembl ENSG00000169432 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv9362571 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2016-06-14 criteria provided, single submitter generalized epilepsy with febrile seizures plus germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Congenital Indifference to Pain germline Detail
Likely benign 2016-06-14 criteria provided, single submitter paroxysmal extreme pain disorder germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Inherited Erythromelalgia germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Small fiber neuropathy germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Febrile seizures, familial germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Severe myoclonic epilepsy in infancy germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001365536.1(SCN9A):c.2875-5del AND Generalized epilepsy with febrile seizures plus ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Congenital Indifference to Pain ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Paroxysmal extreme pain disorder ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Inherited Erythromelalgia ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Small fiber neuropathy ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Febrile seizures, familial ClinVar Detail
NM_001365536.1(SCN9A):c.2875-5del AND Severe myoclonic epilepsy in infancy ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs774840081 dbSNP
Genome
hg19
Position
chr2:167,129,390-167,129,390
Variant Type
snv
Reference Allele
A
Alternative Allele
-
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1199
Mean of sample read depth (HGVD)
34.49
Standard deviation of sample read depth (HGVD)
17.93
Number of reference allele (HGVD)
2396
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.340283569641367E-4
Gene Symbol (HGVD)
SCN9A
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))
rs774840081
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0025
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
42
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
6126
East Asian Allele Counts (ExAC)
41
East Asian Heterozygous Counts (ExAC)
41
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.006692784851452824
Chromosome Counts in All Race (ExAC)
79300
Allele Counts in All Race (ExAC)
41
Heterozygous Counts in All Race (ExAC)
41
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
5.170239596469105E-4
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