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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs11230664

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:61308900 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.19092 (23973/125568, TOPMED)
C=0.1740 (5455/31354, GnomAD)
C=0.232 (1163/5008, 1000G) (+ 5 more)
C=0.010 (47/4480, Estonian)
C=0.008 (30/3854, ALSPAC)
C=0.006 (23/3708, TWINSUK)
C=0.00 (1/600, NorthernSweden)
C=0.04 (8/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDB1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 11 NC_000011.10:g.61308900T>C
GRCh37.p13 chr 11 NC_000011.9:g.61076372T>C
DDB1 RefSeqGene (LRG_474) NG_032697.2:g.38697A>G
Gene: DDB1, damage specific DNA binding protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DDB1 transcript NM_001923.4:c. N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.80908 C=0.19092
gnomAD - Genomes Global Study-wide 31354 T=0.8260 C=0.1740
gnomAD - Genomes European Sub 18904 T=0.9904 C=0.0096
gnomAD - Genomes African Sub 8668 T=0.412 C=0.588
gnomAD - Genomes East Asian Sub 1556 T=0.965 C=0.035
gnomAD - Genomes Other Sub 1088 T=0.926 C=0.074
gnomAD - Genomes American Sub 848 T=0.95 C=0.05
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.98 C=0.02
1000Genomes Global Study-wide 5008 T=0.768 C=0.232
1000Genomes African Sub 1322 T=0.312 C=0.688
1000Genomes East Asian Sub 1008 T=0.971 C=0.029
1000Genomes Europe Sub 1006 T=0.984 C=0.016
1000Genomes South Asian Sub 978 T=0.84 C=0.16
1000Genomes American Sub 694 T=0.93 C=0.07
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.990 C=0.010
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.992 C=0.008
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.994 C=0.006
Northern Sweden ACPOP Study-wide 600 T=1.00 C=0.00
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.96 C=0.04
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C Note
GRCh38.p12 chr 11 NC_000011.10:g.61308900= NC_000011.10:g.61308900T>C
GRCh37.p13 chr 11 NC_000011.9:g.61076372= NC_000011.9:g.61076372T>C
DDB1 RefSeqGene (LRG_474) NG_032697.2:g.38697= NG_032697.2:g.38697A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

46 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15633471 Feb 27, 2004 (120)
2 SC_SNP ss18710651 Feb 27, 2004 (120)
3 EGP_SNPS ss35521795 May 24, 2005 (125)
4 ILLUMINA ss75044968 Dec 06, 2007 (129)
5 CGM_KYOTO ss76861383 Dec 06, 2007 (129)
6 HGSV ss79042255 Dec 06, 2007 (129)
7 HGSV ss85682037 Dec 15, 2007 (130)
8 1000GENOMES ss114686530 Jan 25, 2009 (130)
9 KRIBB_YJKIM ss119680408 Dec 01, 2009 (131)
10 ILLUMINA-UK ss119861250 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss170048799 Jul 04, 2010 (132)
12 ILLUMINA ss171195047 Jul 04, 2010 (132)
13 BUSHMAN ss202781906 Jul 04, 2010 (132)
14 1000GENOMES ss225273277 Jul 14, 2010 (132)
15 1000GENOMES ss242210849 Jul 15, 2010 (132)
16 GMI ss281033895 May 04, 2012 (137)
17 PJP ss291057695 May 09, 2011 (134)
18 ILLUMINA ss536689495 Sep 08, 2015 (146)
19 TISHKOFF ss562596597 Apr 25, 2013 (138)
20 SSMP ss658107086 Apr 25, 2013 (138)
21 EVA-GONL ss988584469 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1077775624 Aug 21, 2014 (142)
23 1000GENOMES ss1341511313 Aug 21, 2014 (142)
24 DDI ss1426651945 Apr 01, 2015 (144)
25 EVA_DECODE ss1598246972 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1626714289 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1669708322 Apr 01, 2015 (144)
28 EVA_MGP ss1711295011 Apr 01, 2015 (144)
29 EVA_SVP ss1713258540 Apr 01, 2015 (144)
30 HAMMER_LAB ss1806841967 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1931943573 Feb 12, 2016 (147)
32 JJLAB ss2026718575 Sep 14, 2016 (149)
33 HUMAN_LONGEVITY ss2182814833 Dec 20, 2016 (150)
34 TOPMED ss2346250970 Dec 20, 2016 (150)
35 GRF ss2699310753 Nov 08, 2017 (151)
36 GNOMAD ss2900322959 Nov 08, 2017 (151)
37 SWEGEN ss3008191889 Nov 08, 2017 (151)
38 TOPMED ss3146895716 Nov 08, 2017 (151)
39 ILLUMINA ss3626669796 Oct 12, 2018 (152)
40 ILLUMINA ss3637909523 Oct 12, 2018 (152)
41 ILLUMINA ss3642907759 Oct 12, 2018 (152)
42 OMUKHERJEE_ADBS ss3646427135 Oct 12, 2018 (152)
43 EGCUT_WGS ss3675530053 Jul 13, 2019 (153)
44 ACPOP ss3738231121 Jul 13, 2019 (153)
45 EVA ss3749369721 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3814713981 Jul 13, 2019 (153)
47 1000Genomes NC_000011.9 - 61076372 Oct 12, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 61076372 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000011.9 - 61076372 Oct 12, 2018 (152)
50 gnomAD - Genomes NC_000011.9 - 61076372 Jul 13, 2019 (153)
51 Northern Sweden NC_000011.9 - 61076372 Jul 13, 2019 (153)
52 TopMed NC_000011.10 - 61308900 Oct 12, 2018 (152)
53 UK 10K study - Twins NC_000011.9 - 61076372 Oct 12, 2018 (152)
54 A Vietnamese Genetic Variation Database NC_000011.9 - 61076372 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs58488259 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss79042255, ss85682037, ss114686530, ss119861250, ss170048799, ss202781906, ss281033895, ss291057695, ss1598246972, ss1713258540, ss3642907759 NC_000011.8:60832947:T:C NC_000011.10:61308899:T:C (self)
54041976, 30010440, 21268301, 147570064, 11515986, 30010440, 6663262, ss225273277, ss242210849, ss536689495, ss562596597, ss658107086, ss988584469, ss1077775624, ss1341511313, ss1426651945, ss1626714289, ss1669708322, ss1711295011, ss1806841967, ss1931943573, ss2026718575, ss2346250970, ss2699310753, ss2900322959, ss3008191889, ss3626669796, ss3637909523, ss3646427135, ss3675530053, ss3738231121, ss3749369721 NC_000011.9:61076371:T:C NC_000011.10:61308899:T:C (self)
64560805, ss2182814833, ss3146895716, ss3814713981 NC_000011.10:61308899:T:C NC_000011.10:61308899:T:C (self)
ss15633471, ss18710651 NT_033903.6:6249413:T:C NC_000011.10:61308899:T:C (self)
ss35521795, ss75044968, ss76861383, ss119680408, ss171195047 NT_167190.1:6382166:T:C NC_000011.10:61308899:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11230664

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post104+4a6ee9c