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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs5979785

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chrX:12953405 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.298938 (37537/125568, TOPMED)
C=0.276940 (33739/121828, ALFA Project)
C=0.26528 (5759/21709, GnomAD) (+ 10 more)
C=0.4262 (1609/3775, 1000G)
C=0.2735 (1014/3708, TWINSUK)
T=0.1942 (569/2930, KOREAN)
C=0.2686 (776/2889, ALSPAC)
C=0.4232 (882/2084, HGDP_Stanford)
C=0.3993 (753/1886, HapMap)
C=0.124 (44/356, SGDP_PRJ)
C=0.269 (29/108, Qatari)
C=0.12 (5/40, GENOME_DK)
C=0.14 (5/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
4 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 X NC_000023.11:g.12953405C>T
GRCh37.p13 chr X NC_000023.10:g.12971524C>T
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

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 121828 C=0.276940 T=0.723060
European Sub 104748 C=0.269466 T=0.730534
African Sub 5044 C=0.1983 T=0.8017
African Others Sub 142 C=0.155 T=0.845
African American Sub 4902 C=0.1995 T=0.8005
Asian Sub 202 C=0.767 T=0.233
East Asian Sub 132 C=0.826 T=0.174
Other Asian Sub 70 C=0.66 T=0.34
Latin American 1 Sub 92 C=0.20 T=0.80
Latin American 2 Sub 248 C=0.339 T=0.661
South Asian Sub 4856 C=0.4557 T=0.5443
Other Sub 6638 C=0.3078 T=0.6922


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.298938 T=0.701062
ALFA Total Global 121828 C=0.276940 T=0.723060
ALFA European Sub 104748 C=0.269466 T=0.730534
ALFA Other Sub 6638 C=0.3078 T=0.6922
ALFA African Sub 5044 C=0.1983 T=0.8017
ALFA South Asian Sub 4856 C=0.4557 T=0.5443
ALFA Latin American 2 Sub 248 C=0.339 T=0.661
ALFA Asian Sub 202 C=0.767 T=0.233
ALFA Latin American 1 Sub 92 C=0.20 T=0.80
gnomAD - Genomes Global Study-wide 21709 C=0.26528 T=0.73472
gnomAD - Genomes European Sub 13307 C=0.24912 T=0.75088
gnomAD - Genomes African Sub 5841 C=0.1977 T=0.8023
gnomAD - Genomes East Asian Sub 977 C=0.817 T=0.183
gnomAD - Genomes Other Sub 795 C=0.262 T=0.738
gnomAD - Genomes American Sub 612 C=0.399 T=0.601
gnomAD - Genomes Ashkenazi Jewish Sub 177 C=0.220 T=0.780
1000Genomes Global Study-wide 3775 C=0.4262 T=0.5738
1000Genomes African Sub 1003 C=0.2014 T=0.7986
1000Genomes Europe Sub 766 C=0.261 T=0.739
1000Genomes East Asian Sub 764 C=0.831 T=0.169
1000Genomes South Asian Sub 718 C=0.561 T=0.439
1000Genomes American Sub 524 C=0.323 T=0.677
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.2735 T=0.7265
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8058 T=0.1942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 C=0.2686 T=0.7314
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.4232 T=0.5768
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.785 T=0.215
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.365 T=0.635
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.337 T=0.663
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.244 T=0.756
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.252 T=0.748
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.301 T=0.699
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.56 T=0.44
HapMap Global Study-wide 1886 C=0.3993 T=0.6007
HapMap American Sub 766 C=0.431 T=0.569
HapMap African Sub 690 C=0.249 T=0.751
HapMap Asian Sub 254 C=0.791 T=0.209
HapMap Europe Sub 176 C=0.284 T=0.716
SGDP_PRJ Global Study-wide 356 C=0.124 T=0.876
Qatari Global Study-wide 108 C=0.269 T=0.731
The Danish reference pan genome Danish Study-wide 40 C=0.12 T=0.88
Siberian Global Study-wide 36 C=0.14 T=0.86
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 C= T
GRCh38.p12 chr X NC_000023.11:g.12953405= NC_000023.11:g.12953405C>T
GRCh37.p13 chr X NC_000023.10:g.12971524= NC_000023.10:g.12971524C>T
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#.

103 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8270394 Apr 21, 2003 (114)
2 CSHL-HAPMAP ss17288961 Feb 27, 2004 (120)
3 SSAHASNP ss21006313 Apr 05, 2004 (121)
4 ABI ss43607147 Mar 13, 2006 (126)
5 AFFY ss66495668 Nov 29, 2006 (127)
6 ILLUMINA ss66845347 Nov 29, 2006 (127)
7 ILLUMINA ss67431411 Nov 29, 2006 (127)
8 ILLUMINA ss67787878 Nov 29, 2006 (127)
9 PERLEGEN ss69258085 May 16, 2007 (127)
10 ILLUMINA ss70852645 May 23, 2008 (130)
11 ILLUMINA ss71438295 May 16, 2007 (127)
12 ILLUMINA ss75889339 Dec 06, 2007 (129)
13 AFFY ss76318720 Dec 08, 2007 (130)
14 ILLUMINA ss79213312 Dec 14, 2007 (130)
15 KRIBB_YJKIM ss84441813 Dec 14, 2007 (130)
16 1000GENOMES ss112791510 Jan 25, 2009 (130)
17 1000GENOMES ss114458411 Jan 25, 2009 (130)
18 ILLUMINA-UK ss115593253 Feb 03, 2009 (130)
19 ILLUMINA ss122495502 Dec 01, 2009 (131)
20 ILLUMINA ss154347175 Dec 01, 2009 (131)
21 ILLUMINA ss159523514 Dec 01, 2009 (131)
22 ENSEMBL ss161767564 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss164474063 Jul 04, 2010 (132)
24 ILLUMINA ss172074424 Jul 04, 2010 (132)
25 AFFY ss173244302 Jul 04, 2010 (132)
26 ILLUMINA ss173955309 Jul 04, 2010 (132)
27 BUSHMAN ss204161215 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss208878635 Jul 04, 2010 (132)
29 BL ss255918179 May 09, 2011 (134)
30 GMI ss283698213 May 04, 2012 (137)
31 GMI ss287594958 Apr 25, 2013 (138)
32 PJP ss294520944 May 09, 2011 (134)
33 1000GENOMES ss341318270 May 09, 2011 (134)
34 ILLUMINA ss482797915 May 04, 2012 (137)
35 ILLUMINA ss484344478 May 04, 2012 (137)
36 EXOME_CHIP ss491575123 May 04, 2012 (137)
37 ILLUMINA ss537326924 Sep 08, 2015 (146)
38 TISHKOFF ss566771549 Apr 25, 2013 (138)
39 SSMP ss662702412 Apr 25, 2013 (138)
40 ILLUMINA ss780073570 Sep 08, 2015 (146)
41 ILLUMINA ss781881070 Sep 08, 2015 (146)
42 ILLUMINA ss783359184 Sep 08, 2015 (146)
43 ILLUMINA ss825543830 Apr 01, 2015 (144)
44 ILLUMINA ss833034785 Jul 13, 2019 (153)
45 ILLUMINA ss835555371 Sep 08, 2015 (146)
46 JMKIDD_LAB ss1082799219 Aug 21, 2014 (142)
47 DDI ss1432006476 Apr 01, 2015 (144)
48 1000GENOMES ss1553567632 Apr 01, 2015 (144)
49 EVA_GENOME_DK ss1583331596 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1640358054 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1683352087 Apr 01, 2015 (144)
52 ILLUMINA ss1752796434 Sep 08, 2015 (146)
53 ILLUMINA ss1917716044 Feb 12, 2016 (147)
54 WEILL_CORNELL_DGM ss1939156723 Feb 12, 2016 (147)
55 ILLUMINA ss1945968391 Feb 12, 2016 (147)
56 ILLUMINA ss1958173556 Feb 12, 2016 (147)
57 GENOMED ss1971345694 Jul 19, 2016 (147)
58 ILLUMINA ss2094836641 Dec 20, 2016 (150)
59 ILLUMINA ss2095227482 Dec 20, 2016 (150)
60 USC_VALOUEV ss2158956045 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2315779826 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2629667805 Nov 08, 2017 (151)
63 ILLUMINA ss2634940375 Nov 08, 2017 (151)
64 ILLUMINA ss2634940376 Nov 08, 2017 (151)
65 ILLUMINA ss2634940377 Nov 08, 2017 (151)
66 ILLUMINA ss2635201218 Nov 08, 2017 (151)
67 GRF ss2710084868 Nov 08, 2017 (151)
68 GNOMAD ss2976631334 Nov 08, 2017 (151)
69 AFFY ss2985480965 Nov 08, 2017 (151)
70 AFFY ss2986126887 Nov 08, 2017 (151)
71 SWEGEN ss3019652188 Nov 08, 2017 (151)
72 ILLUMINA ss3022990872 Nov 08, 2017 (151)
73 ILLUMINA ss3022990873 Nov 08, 2017 (151)
74 BIOINF_KMB_FNS_UNIBA ss3029009426 Nov 08, 2017 (151)
75 TOPMED ss3605662227 Nov 08, 2017 (151)
76 ILLUMINA ss3630398777 Oct 12, 2018 (152)
77 ILLUMINA ss3632827546 Oct 12, 2018 (152)
78 ILLUMINA ss3635242524 Oct 12, 2018 (152)
79 ILLUMINA ss3638846867 Oct 12, 2018 (152)
80 ILLUMINA ss3639428235 Oct 12, 2018 (152)
81 ILLUMINA ss3639748658 Oct 12, 2018 (152)
82 ILLUMINA ss3640950006 Oct 12, 2018 (152)
83 ILLUMINA ss3642723900 Oct 12, 2018 (152)
84 ILLUMINA ss3643771487 Oct 12, 2018 (152)
85 ILLUMINA ss3645008606 Oct 12, 2018 (152)
86 ILLUMINA ss3653549198 Oct 12, 2018 (152)
87 ILLUMINA ss3653549199 Oct 12, 2018 (152)
88 ILLUMINA ss3654247241 Oct 12, 2018 (152)
89 ILLUMINA ss3726663863 Jul 13, 2019 (153)
90 ILLUMINA ss3744597427 Jul 13, 2019 (153)
91 ILLUMINA ss3745542950 Jul 13, 2019 (153)
92 EVA ss3769932293 Jul 13, 2019 (153)
93 ILLUMINA ss3773034664 Jul 13, 2019 (153)
94 PACBIO ss3788875919 Jul 13, 2019 (153)
95 PACBIO ss3793738487 Jul 13, 2019 (153)
96 PACBIO ss3798623711 Jul 13, 2019 (153)
97 KHV_HUMAN_GENOMES ss3822782698 Jul 13, 2019 (153)
98 EVA ss3836097663 Apr 27, 2020 (154)
99 EVA ss3841666452 Apr 27, 2020 (154)
100 EVA ss3847182986 Apr 27, 2020 (154)
101 HGDP ss3847968199 Apr 27, 2020 (154)
102 SGDP_PRJ ss3891026840 Apr 27, 2020 (154)
103 KRGDB ss3941361830 Apr 27, 2020 (154)
104 1000Genomes NC_000023.10 - 12971524 Oct 12, 2018 (152)
105 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 12971524 Oct 12, 2018 (152)
106 The Danish reference pan genome NC_000023.10 - 12971524 Apr 27, 2020 (154)
107 gnomAD - Genomes NC_000023.10 - 12971524 Jul 13, 2019 (153)
108 HGDP-CEPH-db Supplement 1 NC_000023.9 - 12881445 Apr 27, 2020 (154)
109 HapMap NC_000023.11 - 12953405 Apr 27, 2020 (154)
110 KOREAN population from KRGDB NC_000023.10 - 12971524 Apr 27, 2020 (154)
111 Qatari NC_000023.10 - 12971524 Apr 27, 2020 (154)
112 SGDP_PRJ NC_000023.10 - 12971524 Apr 27, 2020 (154)
113 Siberian NC_000023.10 - 12971524 Apr 27, 2020 (154)
114 TopMed NC_000023.11 - 12953405 Oct 12, 2018 (152)
115 UK 10K study - Twins NC_000023.10 - 12971524 Oct 12, 2018 (152)
116 dbGaP Population Frequency Project NC_000023.11 - 12953405 Apr 27, 2020 (154)
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)
rs56518853 May 23, 2008 (130)
rs56823210 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639428235, ss3639748658 NC_000023.8:12731180:C:T NC_000023.11:12953404:C:T (self)
646091, ss112791510, ss114458411, ss115593253, ss164474063, ss204161215, ss208878635, ss255918179, ss283698213, ss287594958, ss294520944, ss484344478, ss825543830, ss2635201218, ss3643771487, ss3847968199 NC_000023.9:12881444:C:T NC_000023.11:12953404:C:T (self)
81551230, 45050058, 9496533, 222373224, 48539224, 21198645, 43043820, 11472399, 45050058, ss341318270, ss482797915, ss491575123, ss537326924, ss566771549, ss662702412, ss780073570, ss781881070, ss783359184, ss833034785, ss835555371, ss1082799219, ss1432006476, ss1553567632, ss1583331596, ss1640358054, ss1683352087, ss1752796434, ss1917716044, ss1939156723, ss1945968391, ss1958173556, ss1971345694, ss2094836641, ss2095227482, ss2158956045, ss2629667805, ss2634940375, ss2634940376, ss2634940377, ss2710084868, ss2976631334, ss2985480965, ss2986126887, ss3019652188, ss3022990872, ss3022990873, ss3630398777, ss3632827546, ss3635242524, ss3638846867, ss3640950006, ss3642723900, ss3645008606, ss3653549198, ss3653549199, ss3654247241, ss3744597427, ss3745542950, ss3769932293, ss3773034664, ss3788875919, ss3793738487, ss3798623711, ss3836097663, ss3841666452, ss3891026840, ss3941361830 NC_000023.10:12971523:C:T NC_000023.11:12953404:C:T (self)
3949530, 424198212, 334240119, ss2315779826, ss3029009426, ss3605662227, ss3726663863, ss3822782698, ss3847182986 NC_000023.11:12953404:C:T NC_000023.11:12953404:C:T (self)
ss17288961, ss21006313 NT_011757.13:8938088:C:T NC_000023.11:12953404:C:T (self)
ss8270394, ss43607147, ss66495668, ss66845347, ss67431411, ss67787878, ss69258085, ss70852645, ss71438295, ss75889339, ss76318720, ss79213312, ss84441813, ss122495502, ss154347175, ss159523514, ss161767564, ss172074424, ss173244302, ss173955309 NT_167197.1:10853285:C:T NC_000023.11:12953404:C:T (self)
Help

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

4 citations for rs5979785
PMID Title Author Year Journal
19956107 Follow-up of 1715 SNPs from the Wellcome Trust Case Control Consortium genome-wide association study in type I diabetes families. Cooper JD et al. 2009 Genes and immunity
19956109 The Type I Diabetes Genetics Consortium 'Rapid Response' family-based candidate gene study: strategy, genes selection, and main outcome. Julier C et al. 2009 Genes and immunity
20190752 Multiple common variants for celiac disease influencing immune gene expression. Dubois PC et al. 2010 Nature genetics
24367383 Evidence of stage- and age-related heterogeneity of non-HLA SNPs and risk of islet autoimmunity and type 1 diabetes: the diabetes autoimmunity study in the young. Frederiksen BN et al. 2013 Clinical & developmental immunology
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post536+f5d31d6