NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Re-designed RefSNP Report page!
Clean, modern design that makes it easy to find the information that you are looking for. Report any problems by sending us an email.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs3216780                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:106/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/A/G (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:C=0.4523/2265 (1000 Genomes)
C=0.4821/60533 (TOPMED)
HGVS Names
  • CM000667.2:g.150053837_150053838insC
  • CM000667.2:g.150053837_150053838insT
  • NC_000005.10:g.150053837_150053838insC
  • NC_000005.10:g.150053837_150053838insT
  • NC_000005.9:g.149433400_149433401insC
  • NG_012303.1:g.64535_64536insA
  • NG_012303.1:g.64535_64536insG
  • NG_021389.1:g.58232_58233insC
  • NG_021389.1:g.58232_58233insT
  • NM_001288705.1:c.*231_*232insG
  • NM_001288705.2:c.*231_*232insA
  • NM_001288705.2:c.*231_*232insG
  • NM_001349736.1:c.*231_*232insA
  • NM_001349736.1:c.*231_*232insG
  • NM_005211.3:c.*231_*232insA
  • NM_005211.3:c.*231_*232insG
  • NR_109969.1:n.3200_3201insA
  • NR_109969.1:n.3200_3201insG
  • XR_245851.1:n.3167_3168insG
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 ss287782674 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3216780 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
ss4477760YUSUKE|IMS-JST078338fwd/B-/Gcaggggctgggggctgagccctcacccccccctcccctactgttctcatggtgttggcct06/06/0210/10/03106Genomicunknown
ss66537244SHGC|456byFreqfwd/-/Gcaggggctgggggctgagccctcacccccccctcccctactgttctcatggtgttggcct11/01/0612/16/06127Genomicunknown
ss82378111HGSV|Cor19240_DIV_20070510.chr5_149413593-149413594_1rev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg12/02/0712/02/07130Genomicunknown
ss95410344HUMANGENOME_JCVI|1104685235140fwd/-/Gcaggggctgggggctgagccctcacccccccctcccctactgttctcatggtgttggcct03/21/0805/16/14130Genomicunknown
ss155009933GMI|GMI_INDEL-61339rev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg06/24/0906/24/09131Genomicunknown
ss287782674GMI|GMI_NA10851_INDEL_115567rev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg04/26/1012/21/10134Genomicunknown
ss288665368GMI|GMI_AK_INDEL_407721rev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg12/20/1012/25/11137Genomicunknown
ss295250356PJP|DIP_688060_chr5_149413593rev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg01/21/1101/23/11135Genomicunknown
ss3267323461000GENOMES|JPTCHB_chr5_149413593_indelrev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg03/11/1104/02/11135Genomicunknown
ss3267768221000GENOMES|CEU_chr5_149413593_indelrev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg03/11/1104/02/11135Genomicunknown
ss3270081611000GENOMES|YRI_chr5_149413593_indelrev/-/Caggccaacaccatgagaacagtaggggaggggggggtgagggctcagcccccagcccctg03/11/1104/02/11135Genomicunknown
ss4993047931000GENOMES|20110316_indels_chr5_149433400_149433401rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc03/19/1203/19/12137Genomicunknown
ss551554529LUNTER|CEU_5_149413593-149413594rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc11/21/1211/21/12138Genomic95 %
ss551727231LUNTER|YRI_5_149413593-149413594rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc11/21/1211/21/12138Genomic95 %
ss553221744LUNTER|JPTCHB_5_149413593-149413594rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc11/21/1211/21/12138Genomic95 %
ss663570446SSMP|indel_5_149433401rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc12/18/1202/09/15144Genomicunknown
ss666332190BILGI_BIOE|indel_5_149433400-149433401rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc12/26/1212/26/12138Genomicunknown
ss982253340EVA-GONL|EVA-GONL_rs3216780rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc04/23/1404/24/14142Genomicunknown
ss13746656431000GENOMES|PHASE3_V1_29577903byFreqrev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc08/16/1408/07/15142Genomicunknown
ss1576633020EVA_GENOME_DK|EVA_GENOME_DK_gatk_indels_rs3216780rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc02/19/1502/19/15144Genomicunknown
ss1704917950EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_149433400_16372323rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc03/04/1503/07/15144Genomicunknown
ss1704917980EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_149433400_16372323rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc03/04/1503/07/15144Genomicunknown
ss1804136084HAMMER_LAB|Hsieh_3144995rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc07/15/1507/15/15146Genomicunknown
ss2030721929JJLAB|INDEL424263rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc08/30/1608/31/16149Genomicunknown
ss2626169308SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2473202rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc01/06/1701/06/17151Genomicunknown
ss2997996287SWEGEN|NC_000005.9:g.149433400_149433401insCrev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc05/30/1705/30/17151Genomicunknown
ss3064179279MCHAISSO|HG00514605885rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc09/15/1709/15/17151Genomic92 %
ss3066048471MCHAISSO|NA19240766105rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc09/15/1709/15/17151Genomic92 %
ss3482046298TOPMED|TOPMed_freeze_5?chr5:150,053,837-03rev/-/Caacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc10/04/1710/04/17151Genomicunknown
ss3482046299TOPMED|TOPMed_freeze_5?chr5:150,053,837-04rev/-/Taacaccatgagaacagtaggggaggggggggtgagggctcagcccccagc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3216780|allelePos=501|totalLen=1001|taxid=9606|snpclass=2|alleles='-/A/G'|mol=Genomic|build=151
 GGACAGGAGA GAGCGGGTGA GTGGGGTGAG GCTTGGGGTG GGTGGCCGGT AAAGCACGTT
 GGGCTGGGCC TGATGGATCT GGACTGACAG TTTCTGGTCC CTCCCACCCT CAGGACTATA
 CCAATCTGCC GAGCAGCAGC AGAAGCGGTG GCAGCGGCAG CAGCAGCAGT GAGCTGGAGG
 AGGAGAGCTC TAGTGAGCAC CTGACCTGCT GCGAGCAAGG GGATATCGCC CAGCCCTTGC
 TGCAGCCCAA CAACTATCAG TTCTGCTGAG GAGTTGACGA CAGGGAGTAC CACTCTCCCC
 TCCCACAAAC TTCAACTCCT CCATGGATGG GGCGACACGG GGAGAACATA CAAACTCTGC
 CTTCGGTCAT TTCACTCAAC AGCTCGGCCC AGCTCTGAAA CTTGGGAAGG TGAGGGATTC
 AGGGGAGGTC AGAGGATCCC ACTTCCTGAG CATGGGCCAT CACTGCCAGT CAGGGGCTGG
 GGGCTGAGCC CTCACCCCCC
 N
 CCTCCCCTAC TGTTCTCATG GTGTTGGCCT CGTGTTTGCT ATGCCAACTA GTAGAACCTT
 CTTTCCTAAT CCCCTTATCT TCATGGAAAT GGACTGACTT TATGCCTATG AAGTCCCCAG
 GAGCTACACT GATACTGAGA AAACCAGGCT CTTTGGGGCT AGACAGACTG GCAGAGAGTG
 AGATCTCCCT CTCTGAGAGG AGCAGCAGAT GCTCACAGAC CACACTCAGC TCAGGCCCCT
 TGGAGCAGGA TGGCTCCTCT AAGAATCTCA CAGGACCTCT TAGTCTCTGC CCTATACGCC
 GCCTTCACTC CACAGCCTCA CCCCTCCCAC CCCCATACTG GTACTGCTGT AATGAGCCAA
 GTGGCAGCTA AAAGTTGGGG GTGTTCTGCC CAGTCCCGTC ATTCTGGGCT AGAAGGCAGG
 GGACCTTGGC ATGTGGCTGG CCACACCAAG CAGGAAGCAC AAACTCCCCC AAGCTGACTC
 ATCCTAACTA ACAGTCACGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U63963.1
dbSNP Blast Analysis
UniGene Cluster ID
553489

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3216780 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
HWP-
G
ss1374665643EAS 1008AF 0.513900040.48609999
EUR 1006AF 0.418499980.58149999
AFR 1322AF 0.745100020.25490001
AMR 694AF 0.543200020.45679998
SAS 978AF 0.451900010.54809999
ss66537244R24 30AF 0.699999990.30000001
ss95410344J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.495+/-0.0480000

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

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement