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Reference SNP (refSNP) Cluster Report: rs72549387                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:130/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (REV)
Allele Origin:G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:T=0.0004/21 (ExAC)
T=0.0003/4 (GO-ESP)
T=0.0004/44 (TOPMED)
HGVS Names
  • CM000664.2:g.38075218C>T
  • NC_000002.11:g.38302361C>G
  • NC_000002.11:g.38302361C>T
  • NC_000002.12:g.38075218C>T
  • NG_008386.2:g.5884G>A
  • NG_008386.2:g.5884G>C
  • NM_000104.3:c.171G>A
  • NM_000104.3:c.171G>C
  • NP_000095.2:p.Trp57Cys
  • NP_000095.2:p.Trp57Ter
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 ss263193654 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs72549387 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
ss105434430AFFY_DM3_1|DMET3B12494rev/C/Ggcccaccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcggaccgg09/03/0809/03/08130Genomicunknown
ss263193654OMIM-CURATED-RECORDS|10582fwd/TA/Gccggtccgcgcccccgggcccgtttgcgtgccactgatcggaaacgcggcggcggtgggc10/28/1011/04/10133Genomicunknown
ss491317871EXOME_CHIP|stopgl_34098_chr_2_38302361rev/BC/Tgcccaccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcggaccgg03/05/1203/05/12137Genomicunknown
ss712409486NHLBI-ESP|ESP6500SI-chr2-38302361rev/BC/Tgcccaccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcggaccgg02/20/1302/20/13138Genomicunknown
ss780776027ILLUMINA|HumanOmni25Exome-8v1_A_exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/30/1307/09/15146Genomicunknown
ss783455974ILLUMINA|HumanOmniExpressExome-8v1_A_exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/31/1306/19/15146Genomicunknown
ss1603247838EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_38302361_4256509rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg03/04/1503/04/15144Genomicunknown
ss1646241871EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_38302361_4256509rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg03/04/1503/04/15144Genomicunknown
ss1686272111EVA_EXAC|EVA_EXAC_1135555rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg03/04/1503/04/15144Genomicunknown
ss1752355375ILLUMINA|OmniExpressExome-8v1-1_B_exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/27/1506/09/15146Genomicunknown
ss1917748300ILLUMINA|HumanExome-12v1-1_B_exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg10/16/1510/16/15147Genomicunknown
ss1946037839ILLUMINA|HumanCoreExome-12v1-0_C_exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg10/29/1510/29/15147Genomicunknown
ss1958408524ILLUMINA|exm187709-0_B_F_1918943943rev/BC/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg11/13/1511/13/15147Genomicunknown
ss2229222268HUMAN_LONGEVITY|HLI-2-38075218-C-Trev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg11/18/1611/18/16150Genomicunknown
ss2395146175TOPMED|2_38302361_C/Trev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg11/19/1611/19/16150Genomicunknown
ss2732609686GNOMAD|exomes_rs72549387rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/17/1705/17/17151Genomicunknown
ss2746663535GNOMAD|coding_rs72549387rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/17/1705/17/17151Genomicunknown
ss2772048393GNOMAD|rs72549387rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/17/1705/17/17151Genomicunknown
ss2985165057AFFY|Axiom_PsorMich_Affx-52222950rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/24/1705/24/17151Genomicunknown
ss2989311020SWEGEN|NC_000002.11:g.38302361C>Trev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg05/30/1705/30/17151Genomicunknown
ss3021961013ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm187709-0_B_F_1918943943rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg06/28/1706/28/17151Genomicunknown
ss3304618993TOPMED|TOPMed_freeze_5?chr2:38,075,218rev/C/Tccgccgccgcgtttccgatcagtggcacgcaaacgggcccgggggcgcgg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs72549387|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 GAGGCTGGGG TAGGGGCGTG GGGCGCCCGC TCCTGTCTCT GCACCCCTGA GTGTCACGCC
 TTCTCCTCTC TGTCCCCAGC ATGGGCACCA GCCTCAGCCC GAACGACCCT TGGCCGCTAA
 ACCCGCTGTC CATCCAGCAG ACCACGCTCC TGCTACTCCT GTCGGTGCTG GCCACTGTGC
 ATGTGGGCCA GCGGCTGCTG AGGCAACGGA GGCGGCAGCT CCGGTCCGCG CCCCCGGGCC
 CGTTTGCGTG
 V
 CCACTGATCG GAAACGCGGC GGCGGTGGGC CAGGCGGCTC ACCTCTCGTT CGCTCGCCTG
 GCGCGGCGCT ACGGCGACGT TTTCCAGATC CGCCTGGGCA GCTGCCCCAT AGTGGTGCTG
 AATGGCGAGC GCGCCATCCA CCAGGCCCTG GTGCAGCAGG GCTCGGCCTT CGCCGACCGG
 CCGGCCTTCG CCTCCTTCCG TGTGGTGTCC GGCGGCCGCA GCATGGCTTT CGGCCACTAC
 TCGGAGCACT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002
dbSNP Blast Analysis
3D structure mapping
NP_000095  
OMIM
601771.0010

  Population Diversity (Alleles in RefSNP orientation) Note: rs72549387 allele is reverse to the genome back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPA
G
ss1686272111ExAc_Aggregated_Populations118646AF 0.000193850.99980617

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
byClusterbyFreqUNKNOWNUNKNOWNUNKNOWN

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