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Reference SNP (refSNP) Cluster Report: rs148565559                 ** With Uncertain significance allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:With Uncertain significance allele [ClinVar]
MAF/MinorAlleleCount:C=0.0004/2 (1000 Genomes)
C=0.0012/15 (GO-ESP)
C=0.0014/172 (TOPMED)
HGVS Names
  • CM000678.2:g.88837689A>C
  • CM000678.2:g.88837689A>G
  • NC_000016.10:g.88837689A>C
  • NC_000016.10:g.88837689A>G
  • NC_000016.9:g.88904097A>C
  • NC_000016.9:g.88904097A>G
  • NG_008667.1:g.24278T>C
  • NG_008667.1:g.24278T>G
  • NM_000512.4:c.499T>C
  • NM_000512.4:c.499T>G
  • NM_001323543.1:c.-57T>C
  • NM_001323543.1:c.-57T>G
  • NM_001323544.1:c.517T>C
  • NM_001323544.1:c.517T>G
  • NP_000503.1:p.Phe167Leu
  • NP_000503.1:p.Phe167Val
  • NP_001310473.1:p.Phe173Leu
  • NP_001310473.1:p.Phe173Val
  • XP_005256358.1:p.Phe167Leu
  • XP_005256358.1:p.Phe167Val
  • XP_005256359.1:p.Phe173Leu
  • XP_005256359.1:p.Phe173Val
  • XP_011521284.1:p.Phe173Leu
  • XP_011521284.1:p.Phe173Val
  • XP_016878600.1:p.Phe173Leu
  • XP_016878600.1:p.Phe173Val
  • XP_016878601.1:p.Phe173Leu
  • XP_016878601.1:p.Phe173Val
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 ss342437130 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs148565559 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
ss342437130NHLBI-ESP|ESP2500-chr16-88904097byFreqfwd/TA/Ctgggcctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccactcatc03/25/1109/05/14134Genomicunknown
ss4890905581000GENOMES|20110521_exome_218801_chr16_88904097fwd/TA/Ctgggcctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccactcatc02/10/1202/13/12137Genomicunknown
ss491513294EXOME_CHIP|nonsyn_229520_chr_16_88904097fwd/TA/Ctgggcctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccactcatc03/05/1203/05/12137Genomicunknown
ss491724988CLINSEQ_SNP|SNV-chr16-87431598byFreqfwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/06/1209/05/14137Genomicunknown
ss780722178ILLUMINA|HumanOmni25Exome-8v1_A_exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/30/1307/10/15142Genomicunknown
ss783397960ILLUMINA|HumanOmniExpressExome-8v1_A_exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/31/1306/19/15142Genomicunknown
ss992819662EVA-GONL|EVA-GONL_rs148565559fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac04/23/1404/30/14142Genomicunknown
ss13575146921000GENOMES|PHASE3_V1_70998866fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac08/16/1408/16/14142Genomicunknown
ss1635097076EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_16_88904097_39231662fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/04/1503/04/15144Genomicunknown
ss1678091109EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_16_88904097_39231662fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/04/1503/04/15144Genomicunknown
ss1692468279EVA_EXAC|EXAC_0.3.16:g88904097ag>ggfwd/A/Gctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/04/1503/04/15144Genomicunknown
ss1696861426EVA_DECODE|EVA_DECODE_16_87431598_655720_rs148565559fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/02/1503/04/15144Genomicunknown
ss1711440350EVA_MGP|EVA_XIMO_556110fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac03/09/1503/09/15144Genomicunknown
ss1752212385ILLUMINA|OmniExpressExome-8v1-1_B_exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/27/1506/09/15146Genomicunknown
ss1917911568ILLUMINA|HumanExome-12v1-1_B_exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac10/16/1510/16/15147Genomicunknown
ss1946423670ILLUMINA|HumanCoreExome-12v1-0_C_exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac10/29/1510/29/15147Genomicunknown
ss1959710064ILLUMINA|exm1269308-0_T_F_1921722335fwd/TA/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac11/13/1511/13/15147Genomicunknown
ss2214729696HUMAN_LONGEVITY|HLI-16-88837689-A-Cfwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac11/18/1611/18/16150Genomicunknown
ss2379552591TOPMED|16_88904097_A/Cfwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac11/19/1611/19/16150Genomicunknown
ss2742240889GNOMAD|exomes_rs148565559fwd/A/C/Gctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/17/1705/17/17151Genomicunknown
ss2749624885GNOMAD|coding_rs148565559fwd/A/C/Gctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/17/1705/17/17151Genomicunknown
ss2946567758GNOMAD|rs148565559fwd/A/C/Gctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/23/1705/23/17151Genomicunknown
ss2985079769AFFY|Axiom_PsorMich_Affx-52182791fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac05/24/1705/24/17151Genomicunknown
ss3021740327ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm1269308-0_T_F_1921722335fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac06/28/1706/28/17151Genomicunknown
ss3254720295TOPMED|TOPMed_freeze_5?chr16:88,837,689-01fwd/A/Cctggccttgttgtcataaggtccaagtggcagttgggggatccaaaccac10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs148565559|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 GGCTCTGGGG CAAAACTTGG TGGGACAGAA GCCACCAAAC CAAAGCCCTC GGTGCCCGGG
 GACCCAGGGA CAGACCAGCC CTCATGAGTG GCGACTTGAG CCCACCAGTG CTAGAGGCGG
 GGGGCAGGCA CGCCGGGCAC AGCAGTTCAG GACGTGGGAG GGGAAGGGGT GGGGCTCCAT
 TACCTGCCAA CCATCTCCCA GTCCCTGTAC ACAGGGATGT TGGGCCTGGC CTTGTTGTCA
 TAAGGTCCAA
 V
 GTGGCAGTTG GGGGATCCAA ACCACTCATC AAATCCGTGC TTCAGGGGGT GGAACTGGGG
 CCTGTGACCC AGATGCCTGG AAACAGGAAC CCAGGACACT TCAGGGACCC CACGTGGGGA
 CACTCGGAAG TTCTGAGCAG CAACAGATAC CACCTTCACA AAATTCTTGG TAAGACGAGC
 ACCCTCCAGC ACTGAGTATG GGCTATGCCT GGGCACGGCA GGGACAAAAG ACCAAGGCCT
 CACCCGAGGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000016
dbSNP Blast Analysis
3D structure mapping
NP_000503  

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

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss1357514692EAS 1008AF 1.00000000
EUR 1006AF 0.999000010.00100000
AFR 1322AF 1.00000000
AMR 694AF 0.998599950.00140000
SAS 978AF 1.00000000
ss342437130ESP_Cohort_Populations 4552GF0.997363810.00263620 1.000000000.998681900.00131810
ss491724988CSAgilent 1165GF0.995000060.00500000 1.000000000.997500000.00250000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0200000

  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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