chr17:28525011:A>C Detail (hg19) (SLC6A4)

Information

Genome

Assembly Position
hg19 chr17:28,525,011-28,525,011
hg38 chr17:30,197,993-30,197,993 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001045.5:c.*463T>G
Ensemble ENST00000650711.1:c.*463T>G
ENST00000261707.7:c.*463T>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.826
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 182138 OMIM
HGNC 11050 HGNC
Ensembl ENSG00000108576 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57464542 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 Behavior disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.215 Alcoholic Intoxication, Chronic Subsequent analysis of these two interaction models revealed an OR of 2.71 and 2... BeFree 23757001 Detail
0.003 Alcoholic Intoxication, Chronic Subsequent analysis of these two interaction models revealed an OR of 2.71 and 2... BeFree 23757001 Detail
0.137 autistic disorder Analyzing four markers in SLC6A4 and four markers in ITGB3 in 117 white family t... BeFree 17999363 Detail
0.001 Headache Although a minor contribution of SLC6A4 variants in the genetic liability of MOH... BeFree 21585624 Detail
0.268 autistic disorder Analyzing four markers in SLC6A4 and four markers in ITGB3 in 117 white family t... BeFree 17999363 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001045.6(SLC6A4):c.*463T>G AND Behavior disorder ClinVar Detail
Subsequent analysis of these two interaction models revealed an OR of 2.71 and 2.80, respectively, f... DisGeNET Detail
Subsequent analysis of these two interaction models revealed an OR of 2.71 and 2.80, respectively, f... DisGeNET Detail
Analyzing four markers in SLC6A4 and four markers in ITGB3 in 117 white family triads with autism an... DisGeNET Detail
Although a minor contribution of SLC6A4 variants in the genetic liability of MOH cannot be excluded,... DisGeNET Detail
Analyzing four markers in SLC6A4 and four markers in ITGB3 in 117 white family triads with autism an... 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
rs1042173 dbSNP
Genome
hg19
Position
chr17:28,525,011-28,525,011
Variant Type
snv
Reference Allele
A
Alternative Allele
C
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))
rs1042173
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8257
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13839
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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