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Reference SNP (refSNP) Cluster Report: rs1053352                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:cDNA
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.00004/4 (ExAC)
A=0.00009/1 (GO-ESP)
A=0.00002/3 (TOPMED)
HGVS Names
  • CM000663.2:g.25301036G>A
  • NC_000001.10:g.25627527G>A
  • NC_000001.11:g.25301036G>A
  • NG_007494.1:g.33547G>A
  • NM_001127691.2:c.577G>A
  • NM_001282867.1:c.79G>A
  • NM_001282868.1:c.577G>A
  • NM_001282869.1:c.577G>A
  • NM_001282870.1:c.577G>A
  • NM_001282871.1:c.577G>A
  • NM_001282872.1:c.577G>A
  • NM_001321772.1:c.-67+36004C>T
  • NM_016124.4:c.577G>A
  • NP_001121163.1:p.Glu193Lys
  • NP_001269796.1:p.Glu27Lys
  • NP_001269797.1:p.Glu193Lys
  • NP_001269798.1:p.Glu193Lys
  • NP_001269799.1:p.Glu193Lys
  • NP_001269800.1:p.Glu193Lys
  • NP_001269801.1:p.Glu193Lys
  • NP_057208.2:p.Glu193Lys
  • NR_135787.1:n.1215+36004C>T
  • NR_135788.1:n.277+36942C>T
  • NR_135789.1:n.1215+36004C>T
  • XP_005246016.1:p.Glu193Lys
  • XP_005246017.1:p.Glu193Lys
  • XP_005246018.1:p.Glu193Lys
  • XP_005246019.1:p.Glu193Lys
  • XP_005246020.1:p.Glu193Lys
  • XP_016857504.1:p.Glu193Lys
  • XR_946736.1:n.732G>A
  • XR_946737.1:n.732G>A
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 ss24817614 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053352 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
ss1530464LEE|534303fwd/TA/Ggtggcctggtgcctgccaaagcctctacccagggaacggaggataaagatcagagagcaa09/13/0010/10/0386cDNAunknown
ss4419877LEE|e534310fwd/TA/Ggtggcctggtgcctgccaaagcctctacccagggaacggaggataaagatcagacagcaa04/26/0210/10/03106cDNAunknown
ss24817614SEQUENOM|sqnm216606byFreqfwd/TA/Ggtggcctggtgcctgccaaagcctctacccagggaacggaggataaagatcagacagcaa06/18/0408/05/04144cDNAunknown
ss712285190NHLBI-ESP|ESP6500SI-chr1-25627527fwd/TA/Ggtggcctggtgcctgccaaagcctctacccagggaacggaggataaagatcagacagcaa02/20/1302/20/13144Genomicunknown
ss1685398787EVA_EXAC|EVA_EXAC_194605fwd/A/Gctggtgcctgccaaagcctctacccagggaacggaggataaagatcagac03/04/1503/04/15144Genomicunknown
ss2731264771GNOMAD|exomes_rs1053352fwd/A/Gctggtgcctgccaaagcctctacccagggaacggaggataaagatcagac05/17/1705/17/17151Genomicunknown
ss3071294061TOPMED|TOPMed_freeze_5?chr1:25,301,036fwd/A/Gctggtgcctgccaaagcctctacccagggaacggaggataaagatcagac09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053352|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='A/G'|mol=cDNA|build=151
 TATCTTCAAC ACAGACTACC ACATGAACAT GATGCACATC TACGTGTTCG CAGCCTATTT
 TGGGCTGTCT GTGGCCTGGT GCCTGCCAAA GCCTCTACCC
 R
 AGGGAACGGA GGATAAAGAT CAGACAGCAA CGATACCCAG TTTGTCTGCC ATGCTGGGCG
 CCCTCTTCTT GTGGATGTTC TGGCCAAGTT TCAACTCTGC

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm216606 Z97026 Hs.108380
dbSNP Blast Analysis
UniGene Cluster ID
269364 449968

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
G/G
HWPA
G
ss1530464ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1685398787ExAc_Aggregated_Populations111758AF 0.000035790.99996424
ss24817614CEPH 184AF 0.230000000.76999998
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0060000

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

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