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Reference SNP (refSNP) Cluster Report: rs574132670                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:142/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:C:germline
T:germline
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:T=0.00007/9 (ExAC)
T=0.0002/1 (1000 Genomes)
T=0.00002/2 (TOPMED)
HGVS Names
  • CM000663.2:g.11800250C>T
  • NC_000001.10:g.11860307C>T
  • NC_000001.11:g.11800250C>T
  • NG_013351.1:g.10854G>A
  • NM_001330358.1:c.671G>A
  • NM_005957.4:c.548G>A
  • NP_001317287.1:p.Arg224Gln
  • NP_005948.3:p.Arg183Gln
  • XP_005263515.1:p.Arg224Gln
  • XP_005263516.1:p.Arg206Gln
  • XP_005263517.1:p.Arg183Gln
  • XP_005263518.1:p.Arg183Gln
  • XP_005263519.1:p.Arg183Gln
  • XP_005263520.1:p.Arg101Gln
  • XP_011539797.1:p.Arg223Gln
  • XP_011539798.1:p.Arg224Gln
  • XP_016856817.1:p.Arg224Gln
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 ss1751113062 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs574132670 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
ss12897012741000GENOMES|PHASE3_V1_380220fwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc08/16/1408/16/14142Genomicunknown
ss1685304363EVA_EXAC|EXAC_0.3.1:g11860307c>tfwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc03/04/1503/04/15144Genomicunknown
ss1751113062CLINVAR|SCV000218477rev/TA/Gactacgcagtggacctggtgaagcacatccaagtgagtttggtgactactttgacatctg05/19/1505/21/15144Genomicunknown
ss2322244551TOPMED|1_11860307_C/Tfwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc11/19/1611/19/16150Genomicunknown
ss2731121920GNOMAD|exomes_rs574132670fwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc05/17/1705/17/17151Genomicunknown
ss2746215896GNOMAD|coding_rs574132670fwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc05/17/1705/17/17151Genomicunknown
ss2751674361GNOMAD|rs574132670fwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc05/17/1705/17/17151Genomicunknown
ss3068712188TOPMED|TOPMed_freeze_5?chr1:11,800,250fwd/C/Tgtcaaagtagtcaccaaactcacttggatgtgcttcaccaggtccactgc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs574132670|allelePos=51|totalLen=101|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CCAGCCACTC ACCTGCCACA CAGATGTCAA AGTAGTCACC AAACTCACTT
 Y
 GGATGTGCTT CACCAGGTCC ACTGCGTAGT TGAAGCCTCC CTCCTCCTCT

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis
OMIM
236250

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPC
T
ss1289701274EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 0.998999950.00100000
ss1685304363ExAc_Aggregated_Populations121412AF 0.999925850.00007413

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0090000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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