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Reference SNP (refSNP) Cluster Report: rs17580                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:63/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (REV)
Allele Origin:A:germline
T:germline
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:A=0.0201/2437 (ExAC)
A=0.0196/98 (1000 Genomes)
A=0.0306/398 (GO-ESP)
A=0.0307/3857 (TOPMED)
HGVS Names
  • CM000676.2:g.94380925T>A
  • NC_000014.8:g.94847262T>A
  • NC_000014.9:g.94380925T>A
  • NG_008290.1:g.14768A>T
  • NM_000295.4:c.863A>T
  • NM_001002235.2:c.863A>T
  • NM_001002236.2:c.863A>T
  • NM_001127700.1:c.863A>T
  • NM_001127701.1:c.863A>T
  • NM_001127702.1:c.863A>T
  • NM_001127703.1:c.863A>T
  • NM_001127704.1:c.863A>T
  • NM_001127705.1:c.863A>T
  • NM_001127706.1:c.863A>T
  • NM_001127707.1:c.863A>T
  • NP_000286.3:p.Glu288Val
  • NP_001002235.1:p.Glu288Val
  • NP_001002236.1:p.Glu288Val
  • NP_001121172.1:p.Glu288Val
  • NP_001121173.1:p.Glu288Val
  • NP_001121174.1:p.Glu288Val
  • NP_001121175.1:p.Glu288Val
  • NP_001121176.1:p.Glu288Val
  • NP_001121177.1:p.Glu288Val
  • NP_001121178.1:p.Glu288Val
  • NP_001121179.1:p.Glu288Val
  • NT_187601.1:g.1497497T>A
  • XP_016876859.1:p.Glu288Val
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 ss286895097 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17580 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
ss20191WIAF-CSNP|WIAF-12803fwd/BA/Ttgcctgatgaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa11/12/9910/10/0363cDNAunknown
ss3881969SC_JCM|AL117259.5_9637byFreqfwd/BA/Ttgcctgatgaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa09/25/0105/16/04100Genomicunknown
ss24810906SEQUENOM|sqnm196727fwd/BA/Ttgcctgatgaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa06/18/0406/18/04123cDNAunknown
ss69166927PERLEGEN|PGP04780439byFreqrev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca01/30/0703/31/08130Genomicunknown
ss76870357CGM_KYOTO|12832rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca09/12/0709/12/07129cDNAunknown
ss86351683CANCER-GENOME|15288rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca01/25/0801/25/08129Genomicunknown
ss105437598SNP500CANCER|SERPINA1-05byFreqfwd/A/Ttgcctgwygaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa09/05/0809/05/14130Genomicunknown
ss1085764481000GENOMES|CEU.trio.12.15.2008_3105408_chr14_93917015rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca12/16/0812/16/08130Genomicunknown
ss161050217ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP14-93917015-0_T_F_1588117798rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca08/04/0910/05/09131Genomicunknown
ss171529004COMPLETE_GENOMICS|NA20431_36_chr14_93917015rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca10/01/0910/01/09132Genomicunknown
ss2366604901000GENOMES|pilot_1_CEU_6265119_chr14_93917015rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca05/01/1005/01/10132Genomicunknown
ss286895097GMI|GMI_NA10851_SNP_2907888rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca12/17/1012/17/10138Genomicunknown
ss342395152NHLBI-ESP|ESP2500-chr14-94847262byFreqrev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca03/25/1109/05/14134Genomicunknown
ss475893688OMIM-CURATED-RECORDS|NP_000286.3:p.GLU264VALfwd/A/Ttgcctgatgaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa12/13/1112/13/11136Genomicunknown
ss479177169ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc01/30/1208/28/15146Genomicunknown
ss479737607ILLUMINA|HumanOmni2.5-4v1_D_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc01/30/1210/27/16137Genomicunknown
ss483357987ILLUMINA|HumanOmni2.5-4v1_B_SNP14-93917015-0_T_F_1622019262rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc01/30/1210/28/16137Genomicunknown
ss4910752851000GENOMES|20110521_exome_583083_chr14_94847262rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca02/10/1202/22/12137Genomicunknown
ss491489071EXOME_CHIP|nonsyn_205297_chr_14_94847262rev/A/Tttggtgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatcaggca03/05/1203/05/12137Genomicunknown
ss491692501CLINSEQ_SNP|SNV-chr14-93917015byFreqrev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/06/1209/05/14137Genomicunknown
ss533238249ILLUMINA|HumanOmni5-4v1_B_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc06/22/1208/29/15146Genomicunknown
ss537713419NCBI-CURATED-RECORDS|33008fwd/A/Ttgcctgatgaggggaaactacagcacctggaaatgaactcacccacgatatcatcaccaa07/19/1201/04/13137Genomicunknown
ss779481658ILLUMINA|HumanOmni25Exome-8v1_A_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/30/1307/10/15146Genomicunknown
ss781056125ILLUMINA|HumanOmni2.5-4v1_H_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/30/1307/29/15146Genomicunknown
ss834951694ILLUMINA|HumanOmni2.5-8v1_A_kgp11574257-0_T_F_1822065044rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc09/18/1307/29/15146Genomicunknown
ss991464741EVA-GONL|EVA-GONL_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc04/23/1404/30/14142Genomicunknown
ss13522075061000GENOMES|PHASE3_V1_65487159rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc08/16/1408/16/14142Genomicunknown
ss1577440404EVA_GENOME_DK|EVA_GENOME_DK_snv_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc02/19/1502/19/15144Genomicunknown
ss1584091580EVA_FINRISK|EVA_FINRISK_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc02/27/1502/27/15144Genomicunknown
ss1632384255EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_14_94847262_36259042rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/04/1503/04/15144Genomicunknown
ss1675378288EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_14_94847262_36259042rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/04/1503/04/15144Genomicunknown
ss1691612046EVA_EXAC|EVA_EXAC_6897397rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/04/1503/04/15144Genomicunknown
ss1695479542EVA_DECODE|EVA_DECODE_14_93917015_594672_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/02/1503/04/15144Genomicunknown
ss1711381925EVA_MGP|EVA_XIMO_497685rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc03/09/1503/09/15144Genomicunknown
ss1959578855ILLUMINA|14:94847262-T-A-0_T_F_2304286736rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc11/13/1511/13/15147Genomicunknown
ss2028201770JJLAB|SNP8704325rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc08/29/1608/31/16149Genomicunknown
ss2204475981HUMAN_LONGEVITY|HLI-14-94380925-T-Arev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc11/18/1611/18/16150Genomicunknown
ss2368881647TOPMED|14_94847262_T/Arev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc11/19/1611/19/16150Genomicunknown
ss2633190659ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp11574257-0_T_F_18220650rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc02/02/1702/02/17151Genomicunknown
ss2740918099GNOMAD|exomes_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/17/1705/17/17151Genomicunknown
ss2749197678GNOMAD|coding_rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/17/1705/17/17151Genomicunknown
ss2931100223GNOMAD|rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/23/1705/23/17151Genomicunknown
ss2985030364AFFY|Axiom_PsorMich_Affx-11160904rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/24/1705/24/17151Genomicunknown
ss2985662291AFFY|Axiom_Smokesc1_Affx-11160904rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/24/1705/24/17151Genomicunknown
ss3012692637SWEGEN|NC_000014.8:g.94847262T>Arev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc05/30/1705/30/17151Genomicunknown
ss3021596397ILLUMINA|MEGA_Consortium_v2_15070954_A2_14:94847262-T-A-0_T_F_2304286736rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc06/28/1706/28/17151Genomicunknown
ss3218991193TOPMED|TOPMed_freeze_5?chr14:94,380,925rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc10/01/1710/01/17151Genomicunknown
ss3350947695CSHL|rs17580rev/A/Tgatgatatcgtgggtgagttcatttccaggtgctgtagtttcccctcatc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17580|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 AATAAAAATG CACAGCCACG ATGGCATCTC TTAGCCTGAC ATCGCCACGA TGTAGAAATT
 CTGCATCTTC CTCTAGTTTT GAATTATCCC CACACAATCT TTTTCGGCAG CTTGGATGGT
 CAGTTTCAGC ACCTTTTACA GATGATGAAG CTGAGCCTCG AGGGATGTGT GTCGTCAAGG
 GGGCTCAGGG CTTCTCAGGG AGGGGACTCA TGGTTTCTTT ATTCTGCTAC ACTCTTCCAA
 ACCTTCACTC ACCCCTGGTG ATGCCCACCT TCCCCTCTCT CCAGGCAAAT GGGAGAGACC
 CTTTGAAGTC AAGGACACCG AGGAAGAGGA CTTCCACGTG GACCAGGTGA CCACCGTGAA
 GGTGCCTATG ATGAAGCGTT TAGGCATGTT TAACATCCAG CACTGTAAGA AGCTGTCCAG
 CTGGGTGCTG CTGATGAAAT ACCTGGGCAA TGCCACCGCC ATCTTCTTCC TGCCTGATGA
 GGGGAAACTA CAGCACCTGG
 W
 AAATGAACTC ACCCACGATA TCATCACCAA GTTCCTGGAA AATGAAGACA GAAGGTGATT
 CCCCAACCTG AGGGTGACCA AGAAGCTGCC CACACCTCTT AGCCATGTTG GGACTGAGGC
 CCATCAGGAC TGGCCAGAGG GCTGAGGAGG GTGAACCCCA CATCCCTGGG TCACTGCTAC
 TCTGTATAAA CTTGGCTTCC AGAATGAGGC CACCACTGAG TTCAGGCAGC GCCATCCATG
 CTCCATGAGG AGGACAGTAC CCAGGGGTGA GGAGGTAAAG GTCTCGTCCC TGGGGACTTC
 CCACTCCAGT GTGGACACTG TCCCTTCCCA ATATCCAGTG CCCAGGGCAG GGACAGCAGC
 ACCACCACAC GTTCTGGCAG AACCAAAAAG GAACAGATGG GCTTCCTGGC AAAGGCAGCA
 GTGGAGTGTG GAGTTCAAGG GTAGAATGTC CCTGGGGGGA CGGGGGAAGA GCCTGTGTGG
 CAAGGCCCAG AAAAGCAAGG

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm196727 NT_026437.11 AL132708 K02212
dbSNP Blast Analysis
UniGene Cluster ID
525557
3D structure mapping
NP_000286  NP_001002235  NP_001002236  NP_001121172  NP_001121173  NP_001121174  NP_001121175  NP_001121176  NP_001121177  NP_001121178  NP_001121179  
OMIM
107400.0013

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs17580 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/T
T/T
HWPA
T
ss105437598P1 204GF0.970588210.02941176 1.000000000.985294100.01470588
CAUC1 62GF0.935483870.06451613 1.000000000.967741910.03225806
AFR1 48GF1.00000000 1.00000000
HISP1 46GF0.956521750.04347826 1.000000000.978260870.02173913
PAC1 48GF1.00000000 1.00000000
P3 550GF0.974545480.02545455 1.000000000.987272740.01272727
CAUC3 130GF0.892307700.10769231 1.000000000.946153820.05384615
AFR3 146GF1.00000000 1.00000000
HISP3 98GF1.00000000 1.00000000
PAC3 176GF1.00000000 1.00000000
ss1352207506EAS 1008AF 1.00000000
EUR 1006AF 0.943299950.05670000
AFR 1322AF 0.999199990.00080000
AMR 694AF 0.942399980.05760000
SAS 978AF 1.00000000
ss1691612046ExAc_Aggregated_Populations121412AF 0.979927840.02007215
ss171529004PGP 2IG 1.00000000 0.500000000.50000000
ss20191WIAF-CSNP-MITOGPOP4 38AF 0.974999960.02500000
ss236660490pilot_1_CEU_low_coverage_panel 120AF 0.949999990.05000000
ss342395152ESP_Cohort_Populations 4552GF0.945957840.052724080.001318100.342782000.972319840.02768014
ss3881969CEPH 184AF 0.920000020.08000000
ss491692501CSAgilent 1323GF0.919999960.076999990.003000000.438578000.958500030.04150000
ss69166927HapMap-CEUEuropean 120IG0.899999980.10000000 1.000000000.949999990.05000000
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.039+/-0.1350000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNYESUNKNOWN

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