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Reference SNP (refSNP) Cluster Report: rs146093755                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byCluster
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:T=0.000008/1 (ExAC)
T=0.00008/1 (GO-ESP)
T=0.00005/6 (TOPMED)
HGVS Names
  • CM000678.2:g.88840999C>T
  • NC_000016.10:g.88840999C>T
  • NC_000016.9:g.88907407C>T
  • NG_008667.1:g.20968G>A
  • NM_000512.4:c.415G>A
  • NM_001323543.1:c.-141G>A
  • NM_001323544.1:c.433G>A
  • NP_000503.1:p.Gly139Ser
  • NP_001310473.1:p.Gly145Ser
  • XP_005256358.1:p.Gly139Ser
  • XP_005256359.1:p.Gly145Ser
  • XP_011521284.1:p.Gly145Ser
  • XP_016878600.1:p.Gly145Ser
  • XP_016878601.1:p.Gly145Ser
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss342437132 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs146093755 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss342437132NHLBI-ESP|ESP2500-chr16-88907407fwd/BC/Tgcaggcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggccttctt03/25/1103/27/11134Genomicunknown
ss491724989CLINSEQ_SNP|SNV-chr16-87434908fwd/BC/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc03/06/1203/13/12137Genomicunknown
ss1692468323EVA_EXAC|EVA_EXAC_7816794fwd/C/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc03/04/1503/04/15144Genomicunknown
ss2742240954GNOMAD|exomes_rs146093755fwd/C/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc05/17/1705/17/17151Genomicunknown
ss2985079774AFFY|Axiom_PsorMich_Affx-80254947fwd/C/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc05/24/1705/24/17151Genomicunknown
ss3021740335ILLUMINA|MEGA_Consortium_v2_15070954_A2_Variant56134-0_T_R_2308484245fwd/C/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc06/28/1706/28/17151Genomicunknown
ss3254721239TOPMED|TOPMed_freeze_5?chr16:88,840,999fwd/C/Tcgtggccaggagacttaccacttgcgacaatcttgctgacgtagccggcc10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs146093755|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GCGGAGTCTG ATGCCGCAGG ATACTCGCGG CCGTGGGACC AGCCTGGTGA CCTGAGATCC
 TGCTGGCAAG GTCACGCTGG CCTGCACAGG GACGCTGGAG ACACCTGAAC ACACCCAGAA
 TCAGCTGCCG TTTCCCACCC AAGACACCCT CCTCATTTGG AAACTTGTGG CCATGTCCCT
 TGGAACCAAG GCCAGGAAGT GGATGGAGCA GGACGCCTGG GCAGGCGTGG CCAGGAGACT
 TACCACTTGC
 Y
 GACAATCTTG CTGACGTAGC CGGCCTTCTT CAGAAGCTCC GGCAGGAGCT GCTCCGAGTC
 TGGGATGCCG CCCACAATCT CCTGCGGTGT GTAGGCTGGA AGAGCAGCGC TGGGTGAGCC
 CCGAGGAGAC CCCGAGAAGC TGCCACCAAC CCCATCCTAA CAGGACACTG GGGGCTGCGT
 CCACACATCC TAACAGGACA CTGGCCCCTC GGGGTCAAAG GCTGTGCCTG GGGGCTGCGC
 GTCCACAGGG

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis
3D structure mapping
NP_000503  

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1692468323ExAc_Aggregated_Populations121406AF 0.999991770.00000824
ss342437132ESP_Cohort_Populations 4550GF0.999560420.00043956 1.000000000.999780240.00021978
ss491724989CSAgilent 1323GF0.998000030.00200000 1.000000000.999000010.00100000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0030000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterUNKNOWNUNKNOWNUNKNOWN

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