chr12:6457062:T>C Detail (hg19) (SCNN1A)

Information

Genome

Assembly Position
hg19 chr12:6,457,062-6,457,062
hg38 chr12:6,347,896-6,347,896 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001159575.1:c.2056A>G NP_001153047.1:p.Thr686Ala
NM_001159576.1:c.2164A>G NP_001153048.1:p.Thr722Ala
NM_001038.5:c.1987A>G NP_001029.1:p.Thr663Ala
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.662
ToMMo:0.617
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.544

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600228 OMIM
HGNC 10599 HGNC
Ensembl ENSG00000111319 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv44810383 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-03-05 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-15 criteria provided, multiple submitters, no conflicts autosomal recessive pseudohypoaldosteronism type 1 germline Detail
Benign 2021-07-15 criteria provided, multiple submitters, no conflicts Bronchiectasis with or without elevated sweat chloride 2 germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-07-15 criteria provided, single submitter Liddle syndrome 3 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.366 amyotrophic lateral sclerosis Recently, four single nucleotide polymorphisms (SNPs), including rs2814707 in th... BeFree 24493373 Detail
0.003 amyotrophic lateral sclerosis Recently, four single nucleotide polymorphisms (SNPs), including rs2814707 in th... BeFree 24493373 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001038.6(SCNN1A):c.1987A>G (p.Thr663Ala) AND not specified ClinVar Detail
NM_001038.6(SCNN1A):c.1987A>G (p.Thr663Ala) AND Autosomal recessive pseudohypoaldosteronism type 1 ClinVar Detail
NM_001038.6(SCNN1A):c.1987A>G (p.Thr663Ala) AND Bronchiectasis with or without elevated sweat chlori... ClinVar Detail
NM_001038.6(SCNN1A):c.1987A>G (p.Thr663Ala) AND not provided ClinVar Detail
NM_001038.6(SCNN1A):c.1987A>G (p.Thr663Ala) AND Liddle syndrome 3 ClinVar Detail
Recently, four single nucleotide polymorphisms (SNPs), including rs2814707 in the 9p21, rs12608932 i... DisGeNET Detail
Recently, four single nucleotide polymorphisms (SNPs), including rs2814707 in the 9p21, rs12608932 i... 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
rs2228576 dbSNP
Genome
hg19
Position
chr12:6,457,062-6,457,062
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
979
Mean of sample read depth (HGVD)
10.95
Standard deviation of sample read depth (HGVD)
5.77
Number of reference allele (HGVD)
662
Number of alternative allele (HGVD)
1294
Allele Frequency (HGVD)
0.6615541922290389
Gene Symbol (HGVD)
SCNN1A
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))
rs2228576
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6166
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10335
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
6930
East Asian Allele Counts (ExAC)
3772
East Asian Heterozygous Counts (ExAC)
1884
East Asian Homozygous Counts (ExAC)
944
East Asian Allele Frequency (ExAC)
0.5443001443001443
Chromosome Counts in All Race (ExAC)
89108
Allele Counts in All Race (ExAC)
63561
Heterozygous Counts in All Race (ExAC)
19391
Homozygous Counts in All Race (ExAC)
22085
Allele Frequency in All Race (ExAC)
0.7133029582080173
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