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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.

rs7966851

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:132200563 (GRCh38.p14) 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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.228278 (60423/264690, TOPMED)
G=0.39079 (11043/28258, 14KJPN)
G=0.39732 (6659/16760, 8.3KJPN) (+ 12 more)
G=0.2653 (2016/7600, ALFA)
G=0.2470 (1582/6404, 1000G_30x)
G=0.2460 (1232/5008, 1000G)
G=0.1984 (889/4480, Estonian)
G=0.4038 (1183/2930, KOREAN)
G=0.3914 (717/1832, Korea1K)
G=0.191 (191/998, GoNL)
G=0.207 (124/600, NorthernSweden)
G=0.230 (115/500, SGDP_PRJ)
G=0.255 (55/216, Qatari)
G=0.252 (54/214, Vietnamese)
G=0.25 (12/48, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GALNT9 : Intron Variant
LOC105370091 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 7600 G=0.2653 A=0.0000, C=0.7347
European Sub 6994 G=0.2415 A=0.0000, C=0.7585
African Sub 280 G=0.629 A=0.000, C=0.371
African Others Sub 10 G=0.4 A=0.0, C=0.6
African American Sub 270 G=0.637 A=0.000, C=0.363
Asian Sub 22 G=0.95 A=0.00, C=0.05
East Asian Sub 18 G=0.94 A=0.00, C=0.06
Other Asian Sub 4 G=1.0 A=0.0, C=0.0
Latin American 1 Sub 6 G=1.0 A=0.0, C=0.0
Latin American 2 Sub 32 G=1.00 A=0.00, C=0.00
South Asian Sub 12 G=0.67 A=0.00, C=0.33
Other Sub 254 G=0.331 A=0.000, C=0.669


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 264690 G=0.228278 C=0.771722
14KJPN JAPANESE Study-wide 28258 G=0.39079 C=0.60921
8.3KJPN JAPANESE Study-wide 16760 G=0.39732 C=0.60268
Allele Frequency Aggregator Total Global 7600 G=0.2653 A=0.0000, C=0.7347
Allele Frequency Aggregator European Sub 6994 G=0.2415 A=0.0000, C=0.7585
Allele Frequency Aggregator African Sub 280 G=0.629 A=0.000, C=0.371
Allele Frequency Aggregator Other Sub 254 G=0.331 A=0.000, C=0.669
Allele Frequency Aggregator Latin American 2 Sub 32 G=1.00 A=0.00, C=0.00
Allele Frequency Aggregator Asian Sub 22 G=0.95 A=0.00, C=0.05
Allele Frequency Aggregator South Asian Sub 12 G=0.67 A=0.00, C=0.33
Allele Frequency Aggregator Latin American 1 Sub 6 G=1.0 A=0.0, C=0.0
1000Genomes_30x Global Study-wide 6404 G=0.2470 C=0.7530
1000Genomes_30x African Sub 1786 G=0.2402 C=0.7598
1000Genomes_30x Europe Sub 1266 G=0.2156 C=0.7844
1000Genomes_30x South Asian Sub 1202 G=0.2629 C=0.7371
1000Genomes_30x East Asian Sub 1170 G=0.2957 C=0.7043
1000Genomes_30x American Sub 980 G=0.222 C=0.778
1000Genomes Global Study-wide 5008 G=0.2460 C=0.7540
1000Genomes African Sub 1322 G=0.2383 C=0.7617
1000Genomes East Asian Sub 1008 G=0.2966 C=0.7034
1000Genomes Europe Sub 1006 G=0.2237 C=0.7763
1000Genomes South Asian Sub 978 G=0.249 C=0.751
1000Genomes American Sub 694 G=0.215 C=0.785
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.1984 C=0.8016
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4038 C=0.5962
Korean Genome Project KOREAN Study-wide 1832 G=0.3914 C=0.6086
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.191 C=0.809
Northern Sweden ACPOP Study-wide 600 G=0.207 C=0.793
SGDP_PRJ Global Study-wide 500 G=0.230 C=0.770
Qatari Global Study-wide 216 G=0.255 C=0.745
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.252 C=0.748
Siberian Global Study-wide 48 G=0.25 C=0.75
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.p14 chr 12 NC_000012.12:g.132200563G>A
GRCh38.p14 chr 12 NC_000012.12:g.132200563G>C
GRCh37.p13 chr 12 NC_000012.11:g.132685108G>A
GRCh37.p13 chr 12 NC_000012.11:g.132685108G>C
GRCh38.p14 chr 12 fix patch HG2246_HG2248_HG2276_PATCH NW_021160007.1:g.107592G>A
GRCh38.p14 chr 12 fix patch HG2246_HG2248_HG2276_PATCH NW_021160007.1:g.107592G>C
Gene: GALNT9, polypeptide N-acetylgalactosaminyltransferase 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GALNT9 transcript variant A NM_001122636.2:c.1401+561…

NM_001122636.2:c.1401+561C>T

N/A Intron Variant
GALNT9 transcript variant B NM_021808.3:c.303+561C>T N/A Intron Variant
Gene: LOC105370091, uncharacterized LOC105370091 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105370091 transcript variant X1 XR_007063539.1:n. N/A Intron Variant
LOC105370091 transcript variant X2 XR_007063540.1:n. N/A Intron Variant
LOC105370091 transcript variant X3 XR_007063541.1:n. N/A Intron Variant
LOC105370091 transcript variant X4 XR_007063542.1:n. 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

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 G= A C
GRCh38.p14 chr 12 NC_000012.12:g.132200563= NC_000012.12:g.132200563G>A NC_000012.12:g.132200563G>C
GRCh37.p13 chr 12 NC_000012.11:g.132685108= NC_000012.11:g.132685108G>A NC_000012.11:g.132685108G>C
GRCh38.p14 chr 12 fix patch HG2246_HG2248_HG2276_PATCH NW_021160007.1:g.107592= NW_021160007.1:g.107592G>A NW_021160007.1:g.107592G>C
GALNT9 transcript variant A NM_001122636.1:c.324+561= NM_001122636.1:c.324+561C>T NM_001122636.1:c.324+561C>G
GALNT9 transcript variant A NM_001122636.2:c.1401+561= NM_001122636.2:c.1401+561C>T NM_001122636.2:c.1401+561C>G
GALNT9 transcript variant B NM_021808.3:c.303+561= NM_021808.3:c.303+561C>T NM_021808.3:c.303+561C>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#.

75 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss12201386 Jul 11, 2003 (116)
2 SC_SNP ss15838515 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19234739 Feb 27, 2004 (120)
4 SSAHASNP ss20863447 Apr 05, 2004 (121)
5 HGSV ss77439075 Dec 06, 2007 (129)
6 HGSV ss78925853 Dec 06, 2007 (129)
7 HGSV ss83395500 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss89488679 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss97265664 Feb 05, 2009 (130)
10 BGI ss105143457 Dec 01, 2009 (131)
11 1000GENOMES ss112567423 Jan 25, 2009 (130)
12 1000GENOMES ss114330613 Jan 25, 2009 (130)
13 ILLUMINA-UK ss119803587 Dec 01, 2009 (131)
14 ENSEMBL ss133446517 Dec 01, 2009 (131)
15 ENSEMBL ss137530354 Dec 01, 2009 (131)
16 GMI ss158082381 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss168799913 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss171212529 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss175316204 Jul 04, 2010 (132)
20 BUSHMAN ss198897853 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss208289127 Jul 04, 2010 (132)
22 1000GENOMES ss226049833 Jul 14, 2010 (132)
23 1000GENOMES ss236152005 Jul 15, 2010 (132)
24 1000GENOMES ss242668320 Jul 15, 2010 (132)
25 BL ss255401065 May 09, 2011 (134)
26 GMI ss281611777 May 04, 2012 (137)
27 GMI ss286655408 Apr 25, 2013 (138)
28 PJP ss291375601 May 09, 2011 (134)
29 TISHKOFF ss563513566 Apr 25, 2013 (138)
30 SSMP ss659098553 Apr 25, 2013 (138)
31 EVA-GONL ss990128683 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1078894790 Aug 21, 2014 (142)
33 1000GENOMES ss1347275064 Aug 21, 2014 (142)
34 DDI ss1427106107 Apr 01, 2015 (144)
35 EVA_DECODE ss1642237350 Apr 01, 2015 (144)
36 HAMMER_LAB ss1807497530 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1933490626 Feb 12, 2016 (147)
38 GENOMED ss1967719116 Jul 19, 2016 (147)
39 JJLAB ss2027500680 Sep 14, 2016 (149)
40 USC_VALOUEV ss2155860896 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2194480940 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2628236400 Nov 08, 2017 (151)
43 GRF ss2700226107 Nov 08, 2017 (151)
44 GNOMAD ss2916960423 Nov 08, 2017 (151)
45 SWEGEN ss3010614671 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3027563657 Nov 08, 2017 (151)
47 CSHL ss3350329731 Nov 08, 2017 (151)
48 URBANLAB ss3649959338 Oct 12, 2018 (152)
49 EGCUT_WGS ss3677910265 Jul 13, 2019 (153)
50 EVA_DECODE ss3694796723 Jul 13, 2019 (153)
51 ACPOP ss3739526582 Jul 13, 2019 (153)
52 EVA ss3751166596 Jul 13, 2019 (153)
53 PACBIO ss3787384634 Jul 13, 2019 (153)
54 PACBIO ss3792460428 Jul 13, 2019 (153)
55 PACBIO ss3797343799 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3816492686 Jul 13, 2019 (153)
57 EVA ss3833414799 Apr 27, 2020 (154)
58 EVA ss3840279767 Apr 27, 2020 (154)
59 EVA ss3845764881 Apr 27, 2020 (154)
60 SGDP_PRJ ss3879458869 Apr 27, 2020 (154)
61 KRGDB ss3928253888 Apr 27, 2020 (154)
62 KOGIC ss3973074942 Apr 27, 2020 (154)
63 TOPMED ss4938050228 Apr 26, 2021 (155)
64 TOMMO_GENOMICS ss5208910776 Apr 26, 2021 (155)
65 1000G_HIGH_COVERAGE ss5292804692 Oct 16, 2022 (156)
66 EVA ss5409258561 Oct 16, 2022 (156)
67 HUGCELL_USP ss5487346315 Oct 16, 2022 (156)
68 1000G_HIGH_COVERAGE ss5591288625 Oct 16, 2022 (156)
69 SANFORD_IMAGENETICS ss5654279834 Oct 16, 2022 (156)
70 TOMMO_GENOMICS ss5759467615 Oct 16, 2022 (156)
71 YY_MCH ss5813790170 Oct 16, 2022 (156)
72 EVA ss5838741976 Oct 16, 2022 (156)
73 EVA ss5850620088 Oct 16, 2022 (156)
74 EVA ss5906666395 Oct 16, 2022 (156)
75 EVA ss5945693546 Oct 16, 2022 (156)
76 1000Genomes NC_000012.11 - 132685108 Oct 12, 2018 (152)
77 1000Genomes_30x NC_000012.12 - 132200563 Oct 16, 2022 (156)
78 Genetic variation in the Estonian population NC_000012.11 - 132685108 Oct 12, 2018 (152)
79 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 423854568 (NC_000012.12:132200562:G:A 2/140174)
Row 423854569 (NC_000012.12:132200562:G:C 108678/140142)

- Apr 26, 2021 (155)
80 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 423854568 (NC_000012.12:132200562:G:A 2/140174)
Row 423854569 (NC_000012.12:132200562:G:C 108678/140142)

- Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000012.11 - 132685108 Apr 27, 2020 (154)
82 KOREAN population from KRGDB NC_000012.11 - 132685108 Apr 27, 2020 (154)
83 Korean Genome Project NC_000012.12 - 132200563 Apr 27, 2020 (154)
84 Northern Sweden NC_000012.11 - 132685108 Jul 13, 2019 (153)
85 Qatari NC_000012.11 - 132685108 Apr 27, 2020 (154)
86 SGDP_PRJ NC_000012.11 - 132685108 Apr 27, 2020 (154)
87 Siberian NC_000012.11 - 132685108 Apr 27, 2020 (154)
88 8.3KJPN NC_000012.11 - 132685108 Apr 26, 2021 (155)
89 14KJPN NC_000012.12 - 132200563 Oct 16, 2022 (156)
90 TopMed NC_000012.12 - 132200563 Apr 26, 2021 (155)
91 A Vietnamese Genetic Variation Database NC_000012.11 - 132685108 Jul 13, 2019 (153)
92 ALFA NC_000012.12 - 132200563 Apr 26, 2021 (155)
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)
rs58964863 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3322195659 NC_000012.12:132200562:G:A NC_000012.12:132200562:G:A (self)
ss77439075, ss78925853, ss83395500 NC_000012.9:131351337:G:C NC_000012.12:132200562:G:C (self)
ss89488679, ss112567423, ss114330613, ss119803587, ss168799913, ss171212529, ss175316204, ss198897853, ss208289127, ss255401065, ss281611777, ss286655408, ss291375601, ss1642237350 NC_000012.10:131251060:G:C NC_000012.12:132200562:G:C (self)
60109588, 23648513, 14890398, 35431282, 12811447, 15532556, 31475849, 8377250, 66880083, 7405506, ss226049833, ss236152005, ss242668320, ss563513566, ss659098553, ss990128683, ss1078894790, ss1347275064, ss1427106107, ss1807497530, ss1933490626, ss1967719116, ss2027500680, ss2155860896, ss2628236400, ss2700226107, ss2916960423, ss3010614671, ss3350329731, ss3677910265, ss3739526582, ss3751166596, ss3787384634, ss3792460428, ss3797343799, ss3833414799, ss3840279767, ss3879458869, ss3928253888, ss5208910776, ss5409258561, ss5654279834, ss5838741976, ss5945693546 NC_000012.11:132685107:G:C NC_000012.12:132200562:G:C (self)
78814560, 29452943, 93304719, 153595885, 3322195659, ss2194480940, ss3027563657, ss3649959338, ss3694796723, ss3816492686, ss3845764881, ss3973074942, ss4938050228, ss5292804692, ss5487346315, ss5591288625, ss5759467615, ss5813790170, ss5850620088, ss5906666395 NC_000012.12:132200562:G:C NC_000012.12:132200562:G:C (self)
ss97265664, ss105143457, ss133446517, ss137530354, ss158082381 NT_009755.19:10104484:G:C NC_000012.12:132200562:G:C (self)
ss12201386, ss15838515, ss19234739, ss20863447 NT_035243.4:654893:G:C NC_000012.12:132200562:G: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 rs7966851

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.post761+d5e8e07