chr2:108608648:A>G Detail (hg19) (SLC5A7)

Information

Genome

Assembly Position
hg19 chr2:108,608,648-108,608,648
hg38 chr2:107,992,192-107,992,192 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001305005.2:c.265A>G NP_001291934.1:p.Ile89Val
NM_001305006.2:c.265A>G NP_001291935.1:p.Ile89Val
NM_001305007.2:c.265A>G NP_001291936.1:p.Ile89Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.147
ToMMo:0.142
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.130

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 608761 OMIM
HGNC 14025 HGNC
Ensembl ENSG00000115665 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv8112879 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter congenital myasthenic syndrome 20,Neuronopathy, distal hereditary motor, type 7A germline Detail
Benign 2024-02-01 criteria provided, single submitter congenital myasthenic syndrome 20,Neuronopathy, distal hereditary motor, type 7A germline Detail
Benign 2023-11-22 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Recurrent depression MPT analyses show significant associations of the norepinephrine transporter (NE... BeFree 18081710 Detail
<0.001 Recurrent depression MPT analyses show significant associations of the norepinephrine transporter (NE... BeFree 18081710 Detail
<0.001 Recurrent depression MPT analyses show significant associations of the norepinephrine transporter (NE... BeFree 18081710 Detail
<0.001 Recurrent depression MPT analyses show significant associations of the norepinephrine transporter (NE... BeFree 18081710 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_021815.5(SLC5A7):c.265A>G (p.Ile89Val) AND not specified ClinVar Detail
NM_021815.5(SLC5A7):c.265A>G (p.Ile89Val) AND multiple conditions ClinVar Detail
NM_021815.5(SLC5A7):c.265A>G (p.Ile89Val) AND multiple conditions ClinVar Detail
NM_021815.5(SLC5A7):c.265A>G (p.Ile89Val) AND not provided ClinVar Detail
MPT analyses show significant associations of the norepinephrine transporter (NET, SLC6A2) -182 T/C ... DisGeNET Detail
MPT analyses show significant associations of the norepinephrine transporter (NET, SLC6A2) -182 T/C ... DisGeNET Detail
MPT analyses show significant associations of the norepinephrine transporter (NET, SLC6A2) -182 T/C ... DisGeNET Detail
MPT analyses show significant associations of the norepinephrine transporter (NET, SLC6A2) -182 T/C ... 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
rs1013940 dbSNP
Genome
hg19
Position
chr2:108,608,648-108,608,648
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
90.11
Standard deviation of sample read depth (HGVD)
36.72
Number of reference allele (HGVD)
2064
Number of alternative allele (HGVD)
356
Allele Frequency (HGVD)
0.14710743801652892
Gene Symbol (HGVD)
SLC5A7
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))
rs1013940
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1418
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2376
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
1118
East Asian Heterozygous Counts (ExAC)
966
East Asian Homozygous Counts (ExAC)
76
East Asian Allele Frequency (ExAC)
0.12951807228915663
Chromosome Counts in All Race (ExAC)
121024
Allele Counts in All Race (ExAC)
10185
Heterozygous Counts in All Race (ExAC)
8967
Homozygous Counts in All Race (ExAC)
609
Allele Frequency in All Race (ExAC)
0.0841568614489688
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