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Reference SNP (refSNP) Cluster Report: rs116416205                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
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:G=0.00005/6 (ExAC)
G=0.0002/1 (1000 Genomes)
G=0.00008/1 (GO-ESP)
G=0.00007/9 (TOPMED)
HGVS Names
  • CM000663.2:g.7778136A>G
  • NC_000001.10:g.7838196A>G
  • NC_000001.11:g.7778136A>G
  • NM_004781.3:c.250A>G
  • NP_004772.1:p.Thr84Ala
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 ss217314407 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs116416205 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
ss2173144071000GENOMES|pilot_3_CEU_14_chr1_7760783fwd/TA/Ggttttgttacagatgtgggcaatcgggattctgttctggttatcttcatcatcatcatca04/09/1004/09/10132Genomicunknown
ss4886502041000GENOMES|20110521_exome_1924_chr1_7838196fwd/TA/Ggttttgttacagatgtgggcaatcgggattctgttctggttatcttcatcatcatcatca02/10/1202/13/12137Genomicunknown
ss712270198NHLBI-ESP|ESP6500SI-chr1-7838196fwd/TA/Ggttttgttacagatgtgggcaatcgggattctgttctggttatcttcatcatcatcatca02/20/1302/20/13138Genomicunknown
ss974830670EVA-GONL|EVA-GONL_rs116416205fwd/TA/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat04/23/1404/23/14142Genomicunknown
ss12895826121000GENOMES|PHASE3_V1_256323fwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat08/16/1408/16/14142Genomicunknown
ss1584188840EVA_DECODE|EVA_DECODE_1_7760783_59579_rs116416205fwd/TA/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat03/02/1503/02/15144Genomicunknown
ss1599496386EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_7838196_128948fwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat03/04/1503/04/15144Genomicunknown
ss1642490419EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_7838196_128948fwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat03/04/1503/04/15144Genomicunknown
ss1685278117EVA_EXAC|EVA_EXAC_65698fwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat03/04/1503/04/15144Genomicunknown
ss2159837467HUMAN_LONGEVITY|HLI-1-7778136-A-Gfwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat11/18/1611/18/16150Genomicunknown
ss2731082323GNOMAD|exomes_rs116416205fwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat05/17/1705/17/17151Genomicunknown
ss2986254784SWEGEN|NC_000001.10:g.7838196A>Gfwd/A/Ggttacagatgtgggcaatcgggattctgttctggttatcttcatcatcat05/30/1705/30/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs116416205|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GATAAGTTAC CTTCAGGCCC TAATTGAGAA CATTTAATTT AGGCTTTAGA AATTATTAAT
 TACTCCAGAC TGTATGCACC TGAATTTCCC TTTCAGTGAC TAGATGAATA TTATATAATA
 CTCTTCAACA AGCACATTAT GTCTGCATTT GAAATGTGAT ATGGACATAT GTTTTGTTAC
 AGATGTGGGC AATCGGGATT
 R
 CTGTTCTGGT TATCTTCATC ATCATCATCA TCGGTGAGTT ACCCTTTTCT AAACTGATTG
 GAAAAGTCTT CTCCATGTGT TCACAGACCA TTGATTTTGT GTACAAGAAC TCAGATTAAA
 ATTTCCCTCC GAAATGTTAG TTTTGGCTAG GTGCGGTGAC TCATGCCTGT AATCCCAAAG
 CTTTGGGAGG CCAGGAGTTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis

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

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPA
G
ss1289582612EAS 1008AF 1.00000000
EUR 1006AF 0.999000010.00100000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685278117ExAc_Aggregated_Populations121412AF 0.999950590.00004942
ss217314407pilot_3_CEU_exon_capture_panel 178AF 0.994382020.00561798

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0070000

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