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Reference SNP (refSNP) Cluster Report: rs118204438                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
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=0.00002/2 (ExAC)
A=0.00008/1 (GO-ESP)
A=0.00009/11 (TOPMED)
HGVS Names
  • CM000678.2:g.88841077T>A
  • NC_000016.10:g.88841077T>A
  • NC_000016.9:g.88907485T>A
  • NG_008667.1:g.20890A>T
  • NM_000512.4:c.337A>T
  • NM_001323543.1:c.-219A>T
  • NM_001323544.1:c.355A>T
  • NP_000503.1:p.Ile113Phe
  • NP_001310473.1:p.Ile119Phe
  • XP_005256358.1:p.Ile113Phe
  • XP_005256359.1:p.Ile119Phe
  • XP_011521284.1:p.Ile119Phe
  • XP_016878600.1:p.Ile119Phe
  • XP_016878601.1:p.Ile119Phe
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 ss252841671 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs118204438 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
ss252841671OMIM-CURATED-RECORDS|17229fwd/A/Tgctgctcttccagcctacacaccgcaggagttgtgggcggcatcccagactcggagcagc08/12/1008/12/10132Genomicunknown
ss491724990CLINSEQ_SNP|SNV-chr16-87434986rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga03/06/1203/13/12137Genomicunknown
ss507878458GOLDSTEINLAB|16_87434986_Arev/A/Tgctgctccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaagagcagc04/06/1204/06/12137Genomicunknown
ss713338530NHLBI-ESP|ESP6500SI-chr16-88907485rev/A/Tgctgctccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaagagcagc02/20/1302/20/13138Genomicunknown
ss1692468343EVA_EXAC|EVA_EXAC_7816814rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga03/04/1503/04/15144Genomicunknown
ss1959710071ILLUMINA|16:88907485-A-T-0_T_F_2304267455rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga11/13/1511/13/15147Genomicunknown
ss2214730079HUMAN_LONGEVITY|HLI-16-88841077-T-Arev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga11/18/1611/18/16150Genomicunknown
ss2379552972TOPMED|16_88907485_T/Arev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga11/19/1611/19/16150Genomicunknown
ss2742240981GNOMAD|exomes_rs118204438rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga05/17/1705/17/17151Genomicunknown
ss2749624904GNOMAD|coding_rs118204438rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga05/17/1705/17/17151Genomicunknown
ss2946568220GNOMAD|rs118204438rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga05/23/1705/23/17151Genomicunknown
ss2985079776AFFY|Axiom_PsorMich_Affx-80254950rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga05/24/1705/24/17151Genomicunknown
ss3021740338ILLUMINA|MEGA_Consortium_v2_15070954_A2_16:88907485-A-T-0_T_F_2304267455rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga06/28/1706/28/17151Genomicunknown
ss3254721259TOPMED|TOPMed_freeze_5?chr16:88,841,077rev/A/Ttccgagtctgggatgccgcccacaactcctgcggtgtgtaggctggaaga10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs118204438|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 GGAGTCTGCC CCGTCCCCAC CCTCTGGTGA TGGCACTGGC TCTGAGGGGT GCCTGGAAAA
 ATCTTGGGAA GTGCCATGCC CTGTGGACGC GCAGCCCCCA GGCACAGCCT TTGACCCCGA
 GGGGCCAGTG TCCTGTTAGG ATGTGTGGAC GCAGCCCCCA GTGTCCTGTT AGGATGGGGT
 TGGTGGCAGC TTCTCGGGGT CTCCTCGGGG CTCACCCAGC GCTGCTCTTC CAGCCTACAC
 ACCGCAGGAG
 W
 TTGTGGGCGG CATCCCAGAC TCGGAGCAGC TCCTGCCGGA GCTTCTGAAG AAGGCCGGCT
 ACGTCAGCAA GATTGTCGGC AAGTGGTAAG TCTCCTGGCC ACGCCTGCCC AGGCGTCCTG
 CTCCATCCAC TTCCTGGCCT TGGTTCCAAG GGACATGGCC ACAAGTTTCC AAATGAGGAG
 GGTGTCTTGG GTGGGAAACG GCAGCTGATT CTGGGTGTGT TCAGGTGTCT CCAGCGTCCC
 TGTGCAGGCC

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis
3D structure mapping
NP_000503  
OMIM
612222.0005

  Population Diversity (Alleles in RefSNP orientation) Note: rs118204438 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/T
HWPA
T
ss1692468343ExAc_Aggregated_Populations121394AF 0.999983550.00001648
ss491724990CSAgilent 1323GF0.998000030.002000001.000000000.999000010.00100000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0040000

  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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