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Reference SNP (refSNP) Cluster Report: rs113993960                 ** 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:byClusterWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/CTT (FWD)
Allele Origin:-:germline
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:-=0.0068/823 (ExAC)
-=0.0040/20 (1000 Genomes)
-=0.0657/822 (GO-ESP)
HGVS Names
  • CM000669.2:g.117559592_117559594delCTT
  • NC_000007.13:g.117199646_117199648delCTT
  • NC_000007.14:g.117559592_117559594delCTT
  • NG_016465.4:g.98809_98811delCTT
  • NM_000492.3:c.1521_1523delCTT
  • NP_000483.3:p.Phe508del
  • NR_149084.1:n.221+1139_221+1141delAAG
  • XP_011514053.1:p.Phe538del
  • XP_011514055.1:p.Phe427del
  • XP_011514056.1:p.Phe427del
  • XP_016867188.1:p.Phe427del
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 ss252440416 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs113993960 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
ss252440416SNPEDIA|NG_016465.1:g.84630_84632delCTT_1274304488fwd/-/CTTtatgcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatagatacag07/08/1007/08/10132Genomicunknown
ss263192966NCBI-CURATED-RECORDS|NM_000492.3:c.1521_1523delCTTfwd/-/CTTtatgcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatagatacag10/27/1004/19/12136Genomicunknown
ss4999915471000GENOMES|20110316_indels_chr7_117199644_117199646fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag03/19/1203/20/12136Genomicunknown
ss984713522EVA-GONL|EVA-GONL_rs199826652fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag04/23/1404/24/14136Genomicunknown
ss13775953141000GENOMES|PHASE3_V1_39062099byFreqfwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag08/16/1408/07/15136Genomicunknown
ss1594298901EVA_DECODE|EVA_DECODE_7_116986880_907096_rs113993960fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag03/02/1503/03/15136Genomicunknown
ss1711868788EVA_EXAC|EVA_EXAC_3993861fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag03/04/1503/10/15136Genomicunknown
ss1751113321CLINVAR|SCV000218957fwd/-/TCTttatgcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatagataca05/19/1505/21/15136Genomicunknown
ss1959046051ILLUMINA|7:117199645-ATCT-A-0_P_F_2301512867fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag11/13/1511/05/16136Genomicunknown
ss1959046052ILLUMINA|7:117199646-TCTT-T-0_P_F_2304286831fwd/-/CTTctggcaccattaaagaaaatatcattggtgtttcctatgatgaatataga11/13/1511/05/16147Genomicunknown
ss2030866475JJLAB|INDEL568809fwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag08/30/1608/31/16136Genomicunknown
ss2466658901TOPMED|7_117199644_ATCT/Afwd/-/TCTcctggcaccattaaagaaaatatcattggtgtttcctatgatgaatatag11/20/1611/20/16136Genomicunknown
ss2986049754AFFY|Axiom_Smokesc1_Affx-85755649fwd/-/CTTctggcaccattaaagaaaatatcattggtgtttcctatgatgaatataga05/24/1705/24/17151Genomicunknown
ss3022772847ILLUMINA|MEGA_Consortium_v2_15070954_A2_7:117199646-TCTT-T-0_P_F_23042868fwd/-/CTTctggcaccattaaagaaaatatcattggtgtttcctatgatgaatataga06/28/1706/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs113993960|allelePos=251|totalLen=501|taxid=9606|snpclass=2|alleles='-/CTT'|mol=Genomic|build=151
 AAATGAGTTA ATAGAATCTT TACAAATAAG AATATACACT TCTGCTTAGG ATGATAATTG
 GAGGCAAGTG AATCCTGAGC GTGATTTGAT AATGACCTAA TAATGATGGG TTTTATTTCC
 AGACTTCACT TCTAATGGTG ATTATGGGAG AACTGGAGCC TTCAGAGGGT AAAATTAAGC
 ACAGTGGAAG AATTTCATTC TGTTCTCAGT TTTCCTGGAT TATGCCTGGC ACCATTAAAG
 AAAATATCAT
 N
 TGGTGTTTCC TATGATGAAT ATAGATACAG AAGCGTCATC AAAGCATGCC AACTAGAAGA
 GGTAAGAAAC TATGTGAAAA CTTTTTGATT ATGCATATGA ACCCTTCACA CTACCCAAAT
 TATATATTTG GCTCCATATT CAATCGGTTA GTCTACATAT ATTTATGTTT CCTCTATGGG
 TAAGCTACTG TGAATGGATC AATTAATAAA ACACATGACC TATGCTTTAA GAAGCTTGCA
 AACACATGAA

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis
OMIM
219700
602421.0001

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWP-
TCT
ss1377595314EAS 1008AF 1.00000000
EUR 1006AF 0.008900000.99109995
AFR 1322AF 1.00000000
AMR 694AF 0.010100000.98989999
SAS 978AF 0.004100000.99589998

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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