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Reference SNP (refSNP) Cluster Report: rs846664                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (REV)
Allele Origin:G:germline
T:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:C=0.0260/3151 (ExAC)
C=0.0883/442 (1000 Genomes)
C=0.0936/1217 (GO-ESP)
C=0.0906/11377 (TOPMED)
HGVS Names
  • CM000669.2:g.122995119A>C
  • NC_000007.13:g.122635173A>C
  • NC_000007.14:g.122995119A>C
  • NG_011980.1:g.5582T>G
  • NM_016945.2:c.516T>G
  • NP_058641.1:p.Asn172Lys
Links , Linkout
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 ss48409147 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs846664 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
ss1207336KWOK|OVLP-000804-87912fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca09/02/0010/10/0386Genomic97 %
ss1724862KWOK|OVLP-000925-202658byFreqfwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca10/05/0004/07/0487Genomic97 %
ss3181491GENAISSANCE|GEN3174fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca07/19/0110/10/0398Genomicunknown
ss3802435SC_JCM|AC073311.6_101410rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt09/25/0110/10/03100Genomicunknown
ss14763779SC_SNP|NT_007933.13_47811863rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt11/12/0311/22/03120Genomicunknown
ss32475777GOLD|G516T-K172Nfwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcmgttccaggctcataca12/22/04125Genomicunknown
ss48409147APPLERA_GI|hCV7540222byFreqrev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt09/28/0511/03/06126Genomicunknown
ss69026997PERLEGEN|PGP04652139byFreqrev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt01/30/0708/14/07127Genomicunknown
ss74811396AFFY|SNP_M-185329fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca08/09/0708/09/07128Genomicunknown
ss74882543ILLUMINA|ILMN_Human_1M_rs846664fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca08/28/0708/29/07129Genomicunknown
ss79729796HGSV|Cor18507_SNV_20070510.chr7_122229124rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt11/23/0711/23/07130Genomicunknown
ss116284443ILLUMINA-UK|NA18507_000150327_NCBI36.1_chr7_122422409rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt01/16/0901/17/09130Genomic99 %
ss159715598SEATTLESEQ|TAS2R16-122422409rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt07/10/0907/10/09131Genomicunknown
ss160957515ILLUMINA|HumanOmni1-Quad_v1-0_B_rs846664-128_B_F_1513913331fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca08/04/0910/05/09131Genomicunknown
ss174747448ILLUMINA|Human1M-Duov3_B_rs846664-128_B_F_1513913331fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca10/01/0910/05/09132Genomicunknown
ss198199031BUSHMAN|BUSHMAN-chr7-122422408rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt02/16/1003/06/10132Genomicunknown
ss2233069341000GENOMES|pilot_1_YRI_5116617_chr7_122422409rev/A/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt04/22/1004/22/10132Genomicunknown
ss244238675OMICIA|2010_April_001_098_TAS2R16_604867_0001rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt05/27/1008/29/12137Genomicunknown
ss262861481OMIM-CURATED-RECORDS|12857fwd/BG/Taaacagcactgtaactgacaaacttgaaaatttcatcagtatcagttccaggctcataca09/23/1009/23/10133Genomicunknown
ss342245800NHLBI-ESP|ESP2500-chr7-122635173byFreqrev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt03/25/1109/05/14134Genomicunknown
ss480395662ILLUMINA|HumanOmni2.5-4v1_D_kgp13693651-0_B_R_1828025318rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1210/28/16137Genomicunknown
ss481807492ILLUMINA|HumanOmni2.5-4v1_B_rs846664-128_B_F_1735651254rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1210/29/16137Genomicunknown
ss481839948ILLUMINA|HumanOmniExpress-12v1_C_rs846664-131_B_F_1857526027rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1210/27/16137Genomicunknown
ss482801278ILLUMINA|HumanOmni1-Quad_v1-0_C_rs846664-131_B_F_1865246254rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1208/28/15146Genomicunknown
ss485339224ILLUMINA|HumanOmni2.5-4v1_B_SNP7-122422409-0_B_R_1630194546rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1210/29/16137Genomicunknown
ss485698412ILLUMINA|HumanOmni2.5-4v1_D_rs846664-131_B_F_1857526027rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc01/30/1210/28/16137Genomicunknown
ss4909533061000GENOMES|20110521_exome_461104_chr7_122635173rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt02/10/1202/21/12137Genomicunknown
ss491405108EXOME_CHIP|nonsyn_121334_chr_7_122635173rev/TA/Ctgtatgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgctgttt03/05/1203/05/12137Genomicunknown
ss491914262CLINSEQ_SNP|SNV-chr7-122422409rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/06/1203/13/12137Genomicunknown
ss533716819ILLUMINA|HumanOmni5-4v1_B_kgp13693651-0_B_R_1828025318rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc06/22/1208/29/15146Genomicunknown
ss560277135TISHKOFF|snp_chr7_122635173rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc11/22/1211/23/12138Genomicunknown
ss779081266ILLUMINA|HumanOmni25Exome-8v1_A_kgp13693651-0_B_R_1828025318rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/30/1307/09/15146Genomicunknown
ss780863740ILLUMINA|HumanOmni25Exome-8v1_A_exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/30/1307/09/15146Genomicunknown
ss781220690ILLUMINA|HumanOmni2.5-4v1_H_kgp13693651-0_B_R_1828025318rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/30/1307/29/15146Genomicunknown
ss783294762ILLUMINA|HumanOmni2.5-4v1_H_rs846664-131_B_F_1857526027rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/30/1307/29/15146Genomicunknown
ss783548314ILLUMINA|HumanOmniExpressExome-8v1_A_exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/31/1306/19/15146Genomicunknown
ss832556052ILLUMINA|HumanOmniExpress-12v1_H_rs846664-131_B_F_1857526027rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc09/17/1306/19/15146Genomicunknown
ss834544996ILLUMINA|HumanOmni2.5-8v1_A_kgp13693651-0_B_R_1828025318rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc09/18/1307/29/15146Genomicunknown
ss974465653JMKIDD_LAB|KhoeSan_Exomes_chr7_122635173rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/06/1403/06/14142Genomicunknown
ss1067491704JMKIDD_LAB|HGDP_exomes_chr7_122635173rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc07/09/1407/09/14142Genomicunknown
ss1074947760JMKIDD_LAB|HGDP_WGS_chr7_122635173rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc07/10/1407/11/14142Genomicunknown
ss13269681721000GENOMES|PHASE3_V1_39210835rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc08/16/1408/16/14142Genomicunknown
ss1594339415EVA_DECODE|EVA_DECODE_7_122422409_947610_rs846664rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/02/1503/03/15144Genomicunknown
ss1619125903EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_7_122635173_21700904rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/04/1503/04/15144Genomicunknown
ss1662119936EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_7_122635173_21700904rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/04/1503/04/15144Genomicunknown
ss1688926969EVA_EXAC|EVA_EXAC_4003801rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/04/1503/04/15144Genomicunknown
ss1711178474EVA_MGP|EVA_XIMO_294234rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/09/1503/09/15144Genomicunknown
ss1752661617ILLUMINA|OmniExpressExome-8v1-1_B_exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/27/1506/09/15146Genomicunknown
ss1752661618ILLUMINA|OmniExpressExome-8v1-1_B_rs846664-131_B_F_1866866297rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/27/1506/09/15146Genomicunknown
ss1805200006HAMMER_LAB|Hsieh_4213230rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc07/15/1507/16/15146Genomicunknown
ss1917821622ILLUMINA|HumanExome-12v1-1_B_exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc10/16/1510/16/15147Genomicunknown
ss1928011959WEILL_CORNELL_DGM|SNV:chr7:122635173rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc10/16/1510/17/15147Genomicunknown
ss1946219592ILLUMINA|HumanCoreExome-12v1-0_C_exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc10/29/1510/29/15147Genomicunknown
ss1946219593ILLUMINA|HumanCoreExome-12v1-0_C_rs846664-131_B_F_1866866297rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc10/29/1510/29/15147Genomicunknown
ss1959048025ILLUMINA|exm653927-0_B_R_1918443420rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc11/13/1511/13/15147Genomicunknown
ss1959048026ILLUMINA|rs846664-131_B_F_1900137399rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc11/13/1511/13/15147Genomicunknown
ss2024690848JJLAB|SNP5193403rev/TA/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc08/29/1608/30/16149Genomicunknown
ss2297514626HUMAN_LONGEVITY|HLI-7-122995119-A-Crev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc11/18/1611/18/16150Genomicunknown
ss2466975778TOPMED|7_122635173_A/Crev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc11/20/1611/20/16150Genomicunknown
ss2634655147ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp13693651-0_B_R_18280253rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc02/02/1702/02/17151Genomicunknown
ss2634655148ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs846664-131_B_F_186686629rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc02/02/1702/02/17151Genomicunknown
ss2711120350ILLUMINA|Consortium-OncoArray_15047405_A_rs846664-131_B_F_2196890299rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc03/22/1703/22/17151Genomicunknown
ss2736734669GNOMAD|exomes_rs846664rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/17/1705/17/17151Genomicunknown
ss2747914251GNOMAD|coding_rs846664rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/17/1705/17/17151Genomicunknown
ss2858629706GNOMAD|rs846664rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/19/1705/19/17151Genomicunknown
ss2985418934AFFY|Axiom_PsorMich_Affx-29618129rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/24/1705/24/17151Genomicunknown
ss2986050684AFFY|Axiom_Smokesc1_Affx-29618129rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/24/1705/24/17151Genomicunknown
ss3001965276SWEGEN|NC_000007.13:g.122635173A>Crev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc05/30/1705/30/17151Genomicunknown
ss3022775505ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm653927-0_B_R_1918443420rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc06/28/1706/28/17151Genomicunknown
ss3022775506ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs846664-138_B_F_2269496515rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc06/28/1706/28/17151Genomicunknown
ss3543306140TOPMED|TOPMed_freeze_5?chr7:122,995,119rev/A/Cgagcctggaactgatactgatgaaattttcaagtttgtcagttacagtgc10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs846664|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 TAATTTGAAT TATGTACTTT GCAACTTAAC AATCACCTGG GAATTTTTTA ATATCCTTAC
 ATTCTGGTTA AACAGCTTGC TTACCGTGTT CTACTGCATC AAGGTCTCTT CTTTCACCCA
 TCACATCTTT CTCTGGCTGA GGTGGAGAAT TTTGAGGTTG TTTCCCTGGA TATTACTGGG
 TTCTCTGATG ATTACTTGTG TAACAATCAT CCCTTCAGCT ATTGGGAATT ACATTCAAAT
 TCAGTTACTC ACCATGGAGC ATCTACCAAG AAACAGCACT GTAACTGACA AACTTGAAAA
 K
 TTTCATCAGT ATCAGTTCCA GGCTCATACA GTTGCATTGG TTATTCCTTT CATCCTGTTC
 CTGGCCTCCA CCATCTTTCT CATGGCATCA CTGACCAAGC AGATACAACA TCATAGCACT
 GGTCACTGCA ATCCAAGCAT GAAAGCGCGC TTCACTGCCC TGAGGTCCCT TGCCGTCTTA
 TTTATTGTGT TTACCTCTTA CTTTCTAACC ATACTCATCA CCATTATAGG TACTCTATTT
 GATAAGAGAT GTTGGTTATG GGTCTGGGAA GCTTTTGTCT ATGCTTTCAT CTTAATGCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007933 AC004838 AC073311.3 AC073311.5
dbSNP Blast Analysis
UniGene Cluster ID
272395
OMIM
604867.0001

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs846664 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
G/G
G/T
T/T
HWPA
C
G
T
ss116284443YRI 2IG 1.00000000 1.00000000
ss1326968172EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.322200000.67780000
AMR 694AF 0.021600000.97839999
SAS 978AF 0.001000000.99899995
ss1688926969ExAc_Aggregated_Populations121410AF 0.025961620.97403836
ss1724862SC_12_AAsian 24IG 1.00000000 1.00000000
SC_12_AAAfrican American 18IG 0.222222220.111111110.66666669 0.277777790.72222221
SC_12_CEuropean 8IG 1.00000000 1.00000000
SC_95_CEuropean 88IG 1.00000000 1.00000000
CEPH 184AF 1.00000000
EURAME 32GF 0.250000000.75000000 0.583882000.125000000.87500000
AFRAME 32GF0.50000000 0.50000000 0.001000000.500000000.50000000
ss223306934pilot_1_YRI_low_coverage_panel 118AF 0.491525410.50847459
ss342245800ESP_Cohort_Populations 4548GF 0.029023750.161829380.809146880.00100000 0.109938440.89006156
ss48409147HapMap-CEUEuropean 120IG 1.00000000 1.00000000
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 226IG 0.150442480.442477880.407079640.58388200 0.371681420.62831861
AGI_ASP populationmultiple 74IG 0.027027030.162162150.810810800.34278200 0.108108110.89189190
HAPMAP-ASW 98IG 0.122448980.448979590.428571431.00000000 0.346938790.65306121
HAPMAP-LWK 180IG 0.044444450.311111120.644444471.00000000 0.200000000.80000001
HAPMAP-MEX 100IG 0.080000000.920000021.00000000 0.040000000.95999998
HAPMAP-MKK 286IG 0.076923080.321678310.601398590.20032500 0.237762240.76223779
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss491914262CSAgilent 1323GF 0.002000000.998000031.00000000 0.001000000.99900001
ss69026997HapMap-CEUEuropean 120IG 1.00000000 1.00000000
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 0.150000010.483333320.366666671.00000000 0.391666680.60833335

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.051+/-0.1510000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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