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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.

rs2610746

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:88648215 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.285455 (75557/264690, TOPMED)
T=0.276461 (38688/139940, GnomAD)
T=0.16060 (13697/85284, ALFA) (+ 18 more)
T=0.10818 (3057/28258, 14KJPN)
T=0.10835 (1816/16760, 8.3KJPN)
T=0.2940 (1883/6404, 1000G_30x)
T=0.2833 (1419/5008, 1000G)
T=0.0929 (416/4480, Estonian)
T=0.1165 (449/3854, ALSPAC)
T=0.1259 (467/3708, TWINSUK)
T=0.0867 (254/2930, KOREAN)
T=0.3552 (672/1892, HapMap)
T=0.141 (141/998, GoNL)
T=0.093 (58/626, Chileans)
T=0.143 (86/600, NorthernSweden)
T=0.315 (68/216, Qatari)
T=0.056 (12/216, Vietnamese)
C=0.364 (56/154, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNGTT : 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 85284 C=0.83940 T=0.16060
European Sub 68104 C=0.87839 T=0.12161
African Sub 5186 C=0.3571 T=0.6429
African Others Sub 188 C=0.324 T=0.676
African American Sub 4998 C=0.3583 T=0.6417
Asian Sub 242 C=0.921 T=0.079
East Asian Sub 168 C=0.923 T=0.077
Other Asian Sub 74 C=0.92 T=0.08
Latin American 1 Sub 400 C=0.745 T=0.255
Latin American 2 Sub 3422 C=0.8992 T=0.1008
South Asian Sub 4984 C=0.7837 T=0.2163
Other Sub 2946 C=0.8177 T=0.1823


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 C=0.714545 T=0.285455
gnomAD - Genomes Global Study-wide 139940 C=0.723539 T=0.276461
gnomAD - Genomes European Sub 75858 C=0.88381 T=0.11619
gnomAD - Genomes African Sub 41846 C=0.36983 T=0.63017
gnomAD - Genomes American Sub 13638 C=0.84375 T=0.15625
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8034 T=0.1966
gnomAD - Genomes East Asian Sub 3130 C=0.9326 T=0.0674
gnomAD - Genomes Other Sub 2146 C=0.7628 T=0.2372
Allele Frequency Aggregator Total Global 85284 C=0.83940 T=0.16060
Allele Frequency Aggregator European Sub 68104 C=0.87839 T=0.12161
Allele Frequency Aggregator African Sub 5186 C=0.3571 T=0.6429
Allele Frequency Aggregator South Asian Sub 4984 C=0.7837 T=0.2163
Allele Frequency Aggregator Latin American 2 Sub 3422 C=0.8992 T=0.1008
Allele Frequency Aggregator Other Sub 2946 C=0.8177 T=0.1823
Allele Frequency Aggregator Latin American 1 Sub 400 C=0.745 T=0.255
Allele Frequency Aggregator Asian Sub 242 C=0.921 T=0.079
14KJPN JAPANESE Study-wide 28258 C=0.89182 T=0.10818
8.3KJPN JAPANESE Study-wide 16760 C=0.89165 T=0.10835
1000Genomes_30x Global Study-wide 6404 C=0.7060 T=0.2940
1000Genomes_30x African Sub 1786 C=0.2755 T=0.7245
1000Genomes_30x Europe Sub 1266 C=0.8823 T=0.1177
1000Genomes_30x South Asian Sub 1202 C=0.8053 T=0.1947
1000Genomes_30x East Asian Sub 1170 C=0.9188 T=0.0812
1000Genomes_30x American Sub 980 C=0.887 T=0.113
1000Genomes Global Study-wide 5008 C=0.7167 T=0.2833
1000Genomes African Sub 1322 C=0.2791 T=0.7209
1000Genomes East Asian Sub 1008 C=0.9226 T=0.0774
1000Genomes Europe Sub 1006 C=0.8807 T=0.1193
1000Genomes South Asian Sub 978 C=0.806 T=0.194
1000Genomes American Sub 694 C=0.888 T=0.112
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9071 T=0.0929
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8835 T=0.1165
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8741 T=0.1259
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9133 T=0.0867
HapMap Global Study-wide 1892 C=0.6448 T=0.3552
HapMap American Sub 770 C=0.838 T=0.162
HapMap African Sub 692 C=0.273 T=0.727
HapMap Asian Sub 254 C=0.925 T=0.075
HapMap Europe Sub 176 C=0.858 T=0.142
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.859 T=0.141
Chileans Chilean Study-wide 626 C=0.907 T=0.093
Northern Sweden ACPOP Study-wide 600 C=0.857 T=0.143
Qatari Global Study-wide 216 C=0.685 T=0.315
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.944 T=0.056
SGDP_PRJ Global Study-wide 154 C=0.364 T=0.636
The Danish reference pan genome Danish Study-wide 40 C=0.82 T=0.17
Siberian Global Study-wide 4 C=0.5 T=0.5
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 6 NC_000006.12:g.88648215C>T
GRCh37.p13 chr 6 NC_000006.11:g.89357934C>T
Gene: RNGTT, RNA guanylyltransferase and 5'-phosphatase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RNGTT transcript variant 2 NM_001286426.2:c.1437+301…

NM_001286426.2:c.1437+30138G>A

N/A Intron Variant
RNGTT transcript variant 3 NM_001286428.2:c.1257+301…

NM_001286428.2:c.1257+30138G>A

N/A Intron Variant
RNGTT transcript variant 1 NM_003800.5:c.1506+30138G…

NM_003800.5:c.1506+30138G>A

N/A Intron Variant
RNGTT transcript variant X1 XM_047419442.1:c.1507-124…

XM_047419442.1:c.1507-12436G>A

N/A Intron Variant
RNGTT transcript variant X2 XM_047419443.1:c.1507-124…

XM_047419443.1:c.1507-12436G>A

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 C= T
GRCh38.p14 chr 6 NC_000006.12:g.88648215= NC_000006.12:g.88648215C>T
GRCh37.p13 chr 6 NC_000006.11:g.89357934= NC_000006.11:g.89357934C>T
RNGTT transcript variant 2 NM_001286426.2:c.1437+30138= NM_001286426.2:c.1437+30138G>A
RNGTT transcript variant 3 NM_001286428.2:c.1257+30138= NM_001286428.2:c.1257+30138G>A
RNGTT transcript NM_003800.3:c.1506+30138= NM_003800.3:c.1506+30138G>A
RNGTT transcript variant 1 NM_003800.5:c.1506+30138= NM_003800.5:c.1506+30138G>A
RNGTT transcript variant X1 XM_005248767.1:c.1437+30138= XM_005248767.1:c.1437+30138G>A
RNGTT transcript variant X1 XM_047419442.1:c.1507-12436= XM_047419442.1:c.1507-12436G>A
RNGTT transcript variant X2 XM_047419443.1:c.1507-12436= XM_047419443.1:c.1507-12436G>A
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#.

89 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3674434 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss10327495 Jul 11, 2003 (116)
3 PERLEGEN ss23373223 Sep 20, 2004 (123)
4 ABI ss44754425 Mar 14, 2006 (126)
5 AFFY ss66482525 Nov 29, 2006 (127)
6 AFFY ss76299687 Dec 08, 2007 (130)
7 HGSV ss81311927 Dec 15, 2007 (130)
8 KRIBB_YJKIM ss81829232 Dec 14, 2007 (130)
9 HGSV ss82470257 Dec 15, 2007 (130)
10 HGSV ss82675512 Dec 15, 2007 (130)
11 1000GENOMES ss110502779 Jan 24, 2009 (130)
12 1000GENOMES ss114720082 Jan 25, 2009 (130)
13 ILLUMINA-UK ss116597543 Feb 14, 2009 (130)
14 ILLUMINA ss154223661 Dec 01, 2009 (131)
15 ILLUMINA ss159400179 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss163931597 Jul 04, 2010 (132)
17 ILLUMINA ss171319093 Jul 04, 2010 (132)
18 AFFY ss173176952 Jul 04, 2010 (132)
19 ILLUMINA ss173406770 Jul 04, 2010 (132)
20 BUSHMAN ss202152792 Jul 04, 2010 (132)
21 1000GENOMES ss222528583 Jul 14, 2010 (132)
22 1000GENOMES ss233576994 Jul 15, 2010 (132)
23 1000GENOMES ss240612462 Jul 15, 2010 (132)
24 GMI ss278913305 May 04, 2012 (137)
25 GMI ss285458058 Apr 25, 2013 (138)
26 PJP ss293659624 May 09, 2011 (134)
27 ILLUMINA ss483530113 May 04, 2012 (137)
28 ILLUMINA ss485300304 May 04, 2012 (137)
29 ILLUMINA ss535737648 Sep 08, 2015 (146)
30 TISHKOFF ss559358682 Apr 25, 2013 (138)
31 SSMP ss653352668 Apr 25, 2013 (138)
32 ILLUMINA ss780312130 Sep 08, 2015 (146)
33 ILLUMINA ss782208597 Sep 08, 2015 (146)
34 ILLUMINA ss832911896 Aug 21, 2014 (142)
35 ILLUMINA ss833502726 Aug 21, 2014 (142)
36 ILLUMINA ss835799092 Sep 08, 2015 (146)
37 EVA-GONL ss983210901 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1073816380 Aug 21, 2014 (142)
39 1000GENOMES ss1321182291 Aug 21, 2014 (142)
40 EVA_GENOME_DK ss1581784000 Apr 01, 2015 (144)
41 EVA_DECODE ss1592763172 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1616111610 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1659105643 Apr 01, 2015 (144)
44 EVA_SVP ss1712880284 Apr 01, 2015 (144)
45 HAMMER_LAB ss1804550698 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1926468620 Feb 12, 2016 (147)
47 GENOMED ss1970461255 Jul 19, 2016 (147)
48 JJLAB ss2023877519 Sep 14, 2016 (149)
49 USC_VALOUEV ss2152069513 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2286046121 Dec 20, 2016 (150)
51 ILLUMINA ss2634479829 Nov 08, 2017 (151)
52 GRF ss2707688456 Nov 08, 2017 (151)
53 GNOMAD ss2841964256 Nov 08, 2017 (151)
54 SWEGEN ss2999510316 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3025732700 Nov 08, 2017 (151)
56 CSHL ss3347103193 Nov 08, 2017 (151)
57 ILLUMINA ss3629598200 Oct 12, 2018 (152)
58 ILLUMINA ss3632394783 Oct 12, 2018 (152)
59 ILLUMINA ss3638642967 Oct 12, 2018 (152)
60 ILLUMINA ss3642502673 Oct 12, 2018 (152)
61 URBANLAB ss3648412415 Oct 12, 2018 (152)
62 EGCUT_WGS ss3667391415 Jul 13, 2019 (153)
63 EVA_DECODE ss3717730668 Jul 13, 2019 (153)
64 ACPOP ss3733741403 Jul 13, 2019 (153)
65 EVA ss3765336381 Jul 13, 2019 (153)
66 PACBIO ss3785547421 Jul 13, 2019 (153)
67 PACBIO ss3790887443 Jul 13, 2019 (153)
68 PACBIO ss3795766606 Jul 13, 2019 (153)
69 KHV_HUMAN_GENOMES ss3808487255 Jul 13, 2019 (153)
70 EVA ss3830060215 Apr 26, 2020 (154)
71 EVA ss3838511281 Apr 26, 2020 (154)
72 EVA ss3843959219 Apr 26, 2020 (154)
73 SGDP_PRJ ss3865135294 Apr 26, 2020 (154)
74 KRGDB ss3912028947 Apr 26, 2020 (154)
75 EVA ss4017286628 Apr 26, 2021 (155)
76 TOPMED ss4712140721 Apr 26, 2021 (155)
77 TOMMO_GENOMICS ss5178688888 Apr 26, 2021 (155)
78 1000G_HIGH_COVERAGE ss5269380818 Oct 14, 2022 (156)
79 EVA ss5315172110 Oct 14, 2022 (156)
80 EVA ss5367266320 Oct 14, 2022 (156)
81 HUGCELL_USP ss5466915966 Oct 14, 2022 (156)
82 1000G_HIGH_COVERAGE ss5555800115 Oct 14, 2022 (156)
83 SANFORD_IMAGENETICS ss5640940759 Oct 14, 2022 (156)
84 TOMMO_GENOMICS ss5717209669 Oct 14, 2022 (156)
85 YY_MCH ss5807714928 Oct 14, 2022 (156)
86 EVA ss5842617541 Oct 14, 2022 (156)
87 EVA ss5855464773 Oct 14, 2022 (156)
88 EVA ss5884846787 Oct 14, 2022 (156)
89 EVA ss5969444042 Oct 14, 2022 (156)
90 1000Genomes NC_000006.11 - 89357934 Oct 12, 2018 (152)
91 1000Genomes_30x NC_000006.12 - 88648215 Oct 14, 2022 (156)
92 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 89357934 Oct 12, 2018 (152)
93 Chileans NC_000006.11 - 89357934 Apr 26, 2020 (154)
94 Genetic variation in the Estonian population NC_000006.11 - 89357934 Oct 12, 2018 (152)
95 The Danish reference pan genome NC_000006.11 - 89357934 Apr 26, 2020 (154)
96 gnomAD - Genomes NC_000006.12 - 88648215 Apr 26, 2021 (155)
97 Genome of the Netherlands Release 5 NC_000006.11 - 89357934 Apr 26, 2020 (154)
98 HapMap NC_000006.12 - 88648215 Apr 26, 2020 (154)
99 KOREAN population from KRGDB NC_000006.11 - 89357934 Apr 26, 2020 (154)
100 Northern Sweden NC_000006.11 - 89357934 Jul 13, 2019 (153)
101 Qatari NC_000006.11 - 89357934 Apr 26, 2020 (154)
102 SGDP_PRJ NC_000006.11 - 89357934 Apr 26, 2020 (154)
103 Siberian NC_000006.11 - 89357934 Apr 26, 2020 (154)
104 8.3KJPN NC_000006.11 - 89357934 Apr 26, 2021 (155)
105 14KJPN NC_000006.12 - 88648215 Oct 14, 2022 (156)
106 TopMed NC_000006.12 - 88648215 Apr 26, 2021 (155)
107 UK 10K study - Twins NC_000006.11 - 89357934 Oct 12, 2018 (152)
108 A Vietnamese Genetic Variation Database NC_000006.11 - 89357934 Jul 13, 2019 (153)
109 ALFA NC_000006.12 - 88648215 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)
rs56622202 May 25, 2008 (130)
rs57566288 Feb 27, 2009 (130)
rs60188216 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81311927, ss82470257, ss82675512 NC_000006.9:89414652:C:T NC_000006.12:88648214:C:T (self)
ss110502779, ss114720082, ss116597543, ss163931597, ss202152792, ss278913305, ss285458058, ss293659624, ss485300304, ss1592763172, ss1712880284 NC_000006.10:89414652:C:T NC_000006.12:88648214:C:T (self)
33009144, 18384135, 383573, 13129663, 7948939, 8192527, 19206341, 7026268, 8510550, 17152274, 4585867, 36658195, 18384135, 4086554, ss222528583, ss233576994, ss240612462, ss483530113, ss535737648, ss559358682, ss653352668, ss780312130, ss782208597, ss832911896, ss833502726, ss835799092, ss983210901, ss1073816380, ss1321182291, ss1581784000, ss1616111610, ss1659105643, ss1804550698, ss1926468620, ss1970461255, ss2023877519, ss2152069513, ss2634479829, ss2707688456, ss2841964256, ss2999510316, ss3347103193, ss3629598200, ss3632394783, ss3638642967, ss3642502673, ss3667391415, ss3733741403, ss3765336381, ss3785547421, ss3790887443, ss3795766606, ss3830060215, ss3838511281, ss3865135294, ss3912028947, ss4017286628, ss5178688888, ss5315172110, ss5367266320, ss5640940759, ss5842617541, ss5969444042 NC_000006.11:89357933:C:T NC_000006.12:88648214:C:T (self)
43326050, 232937649, 3187258, 51046773, 549518279, 3505822168, ss2286046121, ss3025732700, ss3648412415, ss3717730668, ss3808487255, ss3843959219, ss4712140721, ss5269380818, ss5466915966, ss5555800115, ss5717209669, ss5807714928, ss5855464773, ss5884846787 NC_000006.12:88648214:C:T NC_000006.12:88648214:C:T (self)
ss10327495 NT_007299.12:27178104:C:T NC_000006.12:88648214:C:T (self)
ss3674434, ss23373223, ss44754425, ss66482525, ss76299687, ss81829232, ss154223661, ss159400179, ss171319093, ss173176952, ss173406770 NT_007299.13:27477767:C:T NC_000006.12:88648214: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.

No publications for rs2610746

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