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Reference SNP (refSNP) Cluster Report: rs55980498                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:A=0.0034/407 (ExAC)
A=0.0010/5 (1000 Genomes)
A=0.0041/50 (GO-ESP)
A=0.0035/441 (TOPMED)
HGVS Names
  • CM000664.2:g.178577205G>A
  • NC_000002.11:g.179441932G>A
  • NC_000002.12:g.178577205G>A
  • NG_011618.3:g.258598C>T
  • NG_051363.1:g.59379G>A
  • NM_001256850.1:c.64207C>T
  • NM_001267550.1:c.69130C>T
  • NM_001267550.2:c.69130C>T
  • NM_003319.4:c.41935C>T
  • NM_133378.4:c.61426C>T
  • NM_133432.3:c.42310C>T
  • NM_133437.4:c.42511C>T
  • NP_001243779.1:p.Pro21403Ser
  • NP_001254479.1:p.Pro23044Ser
  • NP_001254479.2:p.Pro23044Ser
  • NP_003310.4:p.Pro13979Ser
  • NP_596869.4:p.Pro20476Ser
  • NP_597676.3:p.Pro14104Ser
  • NP_597681.4:p.Pro14171Ser
  • NR_038271.1:n.596+5756G>A
  • NR_038272.1:n.2044-5367G>A
  • XP_005246885.1:p.Pro20171Ser
  • XP_005246886.1:p.Pro20154Ser
  • XP_005246887.1:p.Pro9939Ser
  • XP_005246888.1:p.Pro9716Ser
  • XP_016860308.1:p.Pro22675Ser
  • XP_016860309.1:p.Pro21141Ser
  • XP_016860310.1:p.Pro21140Ser
  • XP_016860311.1:p.Pro20154Ser
  • XP_016860312.1:p.Pro14026Ser
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 ss107937934 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs55980498 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
ss74801976CANCER-GENOME|7672fwd/TA/Gcagaaacattactgatttcaacaggacctggggaccaggtacatcaaggactgttacctt07/20/0707/20/07129Genomicunknown
ss107937934RSG_UW|TTN-232146rev/BC/Taaggtaacagtccttgatgtacctggtccccaggtcctgttgaaatcagtaatgtttctg12/08/0812/08/08130Genomicunknown
ss4556518601000GENOMES|20101123_snps_1819090_chr2_179441932fwd/A/Gcagaaacattactgatttcaacaggacctggggaccaggtacatcaaggactgttacctt07/20/1107/20/11135Genomicunknown
ss491327834EXOME_CHIP|nonsyn_44061_chr_2_179441932fwd/TA/Gcagaaacattactgatttcaacaggacctggggaccaggtacatcaaggactgttacctt03/05/1203/05/12137Genomicunknown
ss491795594CLINSEQ_SNP|SNV-chr2-179150178byFreqfwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/06/1209/05/14137Genomicunknown
ss712457592NHLBI-ESP|ESP6500SI-chr2-179441932fwd/TA/Gcagaaacattactgatttcaacaggacctggggaccaggtacatcaaggactgttacctt02/20/1302/20/13138Genomicunknown
ss780807494ILLUMINA|HumanOmni25Exome-8v1_A_exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/30/1307/09/15146Genomicunknown
ss783489206ILLUMINA|HumanOmniExpressExome-8v1_A_exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/31/1306/19/15146Genomicunknown
ss977696603EVA-GONL|EVA-GONL_rs55980498fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt04/23/1404/23/14142Genomicunknown
ss13006192421000GENOMES|PHASE3_V1_11743858fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt08/16/1408/16/14142Genomicunknown
ss1579219565EVA_GENOME_DK|EVA_GENOME_DK_snv_rs55980498fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt02/19/1502/20/15144Genomicunknown
ss1584022354EVA_FINRISK|EVA_FINRISK_rs55980498fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt02/27/1502/27/15144Genomicunknown
ss1587137174EVA_DECODE|EVA_DECODE_2_179150178_1339090_rs55980498fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/02/1503/03/15144Genomicunknown
ss1605251595EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_179441932_6453808fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/04/1503/04/15144Genomicunknown
ss1648245628EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_179441932_6453808fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/04/1503/04/15144Genomicunknown
ss1686620708EVA_EXAC|EVA_EXAC_1512130fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/04/1503/04/15144Genomicunknown
ss1710988837EVA_MGP|EVA_XIMO_105376fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt03/09/1503/09/15144Genomicunknown
ss1752326239ILLUMINA|OmniExpressExome-8v1-1_B_exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/27/1506/09/15146Genomicunknown
ss1815616067EVA_MCP|MOLGENIS_CARDIO_PANEL.2:g179441932g>afwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt08/19/1508/19/15146Genomicunknown
ss1917756741ILLUMINA|HumanExome-12v1-1_B_exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt10/16/1510/16/15147Genomicunknown
ss1920946954WEILL_CORNELL_DGM|SNV:chr2:179441932fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt10/16/1510/16/15147Genomicunknown
ss1946059780ILLUMINA|HumanCoreExome-12v1-0_C_exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt10/29/1510/29/15147Genomicunknown
ss1958483648ILLUMINA|exm246648-0_T_F_1918984419fwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt11/13/1511/13/15147Genomicunknown
ss1998368101ACHAKRAVARTILAB|SNV:chr2:179441932G>Afwd/TA/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/20/1605/20/16147Genomicunknown
ss2236974568HUMAN_LONGEVITY|HLI-2-178577205-G-Afwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt11/18/1611/18/16150Genomicunknown
ss2403398150TOPMED|2_179441932_G/Afwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt11/19/1611/19/16150Genomicunknown
ss2733151621GNOMAD|exomes_rs55980498fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/17/1705/17/17151Genomicunknown
ss2746827438GNOMAD|coding_rs55980498fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/17/1705/17/17151Genomicunknown
ss2783363645GNOMAD|rs55980498fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/17/1705/17/17151Genomicunknown
ss2985193175AFFY|Axiom_PsorMich_Affx-18566246fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/24/1705/24/17151Genomicunknown
ss2990945170SWEGEN|NC_000002.11:g.179441932G>Afwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt05/30/1705/30/17151Genomicunknown
ss3022045514ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm246648-0_T_F_1918984419fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt06/28/1706/28/17151Genomicunknown
ss3331523923TOPMED|TOPMed_freeze_5?chr2:178,577,205fwd/A/Gacattactgatttcaacaggacctggggaccaggtacatcaaggactgtt10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs55980498|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CAGACTGTAC AGGTTCTCCT TTGCCATAGT GGTTTACAGC TGAGACCCGG AAGATGTACT
 CATTTCCTTG GATAAGTTTG GTTGCCACAT GCCTGCAAGA CTGAATATCT TCAGAAACCA
 CTGTCCACAA AAGTCGGCTG GTTTCTCTCT TTTCAAGTAT ATAGGACTTA ATTGGTGAGC
 CGCCATCTTC CAAGGGAGGT GTCCATGTAA GTGTTGCTTT TTCAGCAGAA ACATTACTGA
 TTTCAACAGG ACCTG
 R
 GGGACCAGGT ACATCAAGGA CTGTTACCTT CACATGTTCC ACCTTCGTGC CAAAAGGATT
 GGTAGCAGTG ATGGTATATT CACCCGCATC TTTTCTAGTG GCATACTTGA TAGTAAGCAT
 GGAAGATGTT GGGGTTGAAG TTATCTGAGT GATATCTGAT GGTCTAATGT CTTTTCCTGC
 CTTGGACCAA CTTGATTTTG GAAGGGGTTT GCCAAGAATG CTAATGGCAT TCAAAACAAT
 GGTATCCCCT GCTTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002.9
dbSNP Blast Analysis

  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/G
G/G
HWPA
G
ss107937934MESTRONI_CLINICAL_PANEL 366AF 0.002732240.99726778
ss1300619242EAS 1008AF 1.00000000
EUR 1006AF 0.002000000.99799997
AFR 1322AF 0.001500000.99849999
AMR 694AF 0.001400000.99859995
SAS 978AF 1.00000000
ss1686620708ExAc_Aggregated_Populations120790AF 0.003394320.99660569
ss491795594CSAgilent 593GF0.010000000.990000011.000000000.005000000.99500000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.007+/-0.0580000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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