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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.

rs12126748

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:31062316 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.275568 (72940/264690, TOPMED)
A=0.287056 (40162/139910, GnomAD)
A=0.32361 (21952/67834, ALFA) (+ 17 more)
A=0.00032 (9/28258, 14KJPN)
A=0.00042 (7/16760, 8.3KJPN)
A=0.1994 (1277/6404, 1000G_30x)
A=0.1939 (971/5008, 1000G)
A=0.3663 (1641/4480, Estonian)
A=0.3409 (1314/3854, ALSPAC)
A=0.3514 (1303/3708, TWINSUK)
A=0.0007 (2/2922, KOREAN)
A=0.2358 (490/2078, HGDP_Stanford)
A=0.1989 (294/1478, HapMap)
A=0.323 (322/998, GoNL)
A=0.378 (227/600, NorthernSweden)
A=0.213 (46/216, Qatari)
G=0.394 (74/188, SGDP_PRJ)
A=0.35 (24/68, Ancient Sardinia)
A=0.35 (14/40, GENOME_DK)
G=0.39 (7/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PUM1 : 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 67834 G=0.67639 A=0.32361
European Sub 55538 G=0.66144 A=0.33856
African Sub 4502 G=0.8025 A=0.1975
African Others Sub 170 G=0.794 A=0.206
African American Sub 4332 G=0.8029 A=0.1971
Asian Sub 186 G=0.995 A=0.005
East Asian Sub 146 G=1.000 A=0.000
Other Asian Sub 40 G=0.97 A=0.03
Latin American 1 Sub 244 G=0.758 A=0.242
Latin American 2 Sub 1224 G=0.6781 A=0.3219
South Asian Sub 4952 G=0.7021 A=0.2979
Other Sub 1188 G=0.7214 A=0.2786


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=0.724432 A=0.275568
gnomAD - Genomes Global Study-wide 139910 G=0.712944 A=0.287056
gnomAD - Genomes European Sub 75790 G=0.66083 A=0.33917
gnomAD - Genomes African Sub 41902 G=0.79089 A=0.20911
gnomAD - Genomes American Sub 13622 G=0.68712 A=0.31288
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.7474 A=0.2526
gnomAD - Genomes East Asian Sub 3128 G=0.9981 A=0.0019
gnomAD - Genomes Other Sub 2150 G=0.7265 A=0.2735
Allele Frequency Aggregator Total Global 67834 G=0.67639 A=0.32361
Allele Frequency Aggregator European Sub 55538 G=0.66144 A=0.33856
Allele Frequency Aggregator South Asian Sub 4952 G=0.7021 A=0.2979
Allele Frequency Aggregator African Sub 4502 G=0.8025 A=0.1975
Allele Frequency Aggregator Latin American 2 Sub 1224 G=0.6781 A=0.3219
Allele Frequency Aggregator Other Sub 1188 G=0.7214 A=0.2786
Allele Frequency Aggregator Latin American 1 Sub 244 G=0.758 A=0.242
Allele Frequency Aggregator Asian Sub 186 G=0.995 A=0.005
14KJPN JAPANESE Study-wide 28258 G=0.99968 A=0.00032
8.3KJPN JAPANESE Study-wide 16760 G=0.99958 A=0.00042
1000Genomes_30x Global Study-wide 6404 G=0.8006 A=0.1994
1000Genomes_30x African Sub 1786 G=0.8287 A=0.1713
1000Genomes_30x Europe Sub 1266 G=0.7093 A=0.2907
1000Genomes_30x South Asian Sub 1202 G=0.7837 A=0.2163
1000Genomes_30x East Asian Sub 1170 G=0.9940 A=0.0060
1000Genomes_30x American Sub 980 G=0.657 A=0.343
1000Genomes Global Study-wide 5008 G=0.8061 A=0.1939
1000Genomes African Sub 1322 G=0.8230 A=0.1770
1000Genomes East Asian Sub 1008 G=0.9960 A=0.0040
1000Genomes Europe Sub 1006 G=0.7107 A=0.2893
1000Genomes South Asian Sub 978 G=0.780 A=0.220
1000Genomes American Sub 694 G=0.673 A=0.327
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6337 A=0.3663
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6591 A=0.3409
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6486 A=0.3514
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9993 A=0.0007
HGDP-CEPH-db Supplement 1 Global Study-wide 2078 G=0.7642 A=0.2358
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.977 A=0.023
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.638 A=0.362
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.714 A=0.286
HGDP-CEPH-db Supplement 1 Europe Sub 318 G=0.698 A=0.302
HGDP-CEPH-db Supplement 1 Africa Sub 240 G=0.858 A=0.142
HGDP-CEPH-db Supplement 1 America Sub 214 G=0.626 A=0.374
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.74 A=0.26
HapMap Global Study-wide 1478 G=0.8011 A=0.1989
HapMap African Sub 668 G=0.805 A=0.195
HapMap American Sub 552 G=0.790 A=0.210
HapMap Europe Sub 172 G=0.721 A=0.279
HapMap Asian Sub 86 G=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.677 A=0.323
Northern Sweden ACPOP Study-wide 600 G=0.622 A=0.378
Qatari Global Study-wide 216 G=0.787 A=0.213
SGDP_PRJ Global Study-wide 188 G=0.394 A=0.606
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 68 G=0.65 A=0.35
The Danish reference pan genome Danish Study-wide 40 G=0.65 A=0.35
Siberian Global Study-wide 18 G=0.39 A=0.61
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 1 NC_000001.11:g.31062316G>A
GRCh37.p13 chr 1 NC_000001.10:g.31535163G>A
Gene: PUM1, pumilio RNA binding family member 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PUM1 transcript variant 1 NM_001020658.2:c.-11-2739…

NM_001020658.2:c.-11-2739C>T

N/A Intron Variant
PUM1 transcript variant 2 NM_014676.3:c.-11-2739C>T 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
GRCh38.p14 chr 1 NC_000001.11:g.31062316= NC_000001.11:g.31062316G>A
GRCh37.p13 chr 1 NC_000001.10:g.31535163= NC_000001.10:g.31535163G>A
PUM1 transcript variant 1 NM_001020658.1:c.-11-2739= NM_001020658.1:c.-11-2739C>T
PUM1 transcript variant 1 NM_001020658.2:c.-11-2739= NM_001020658.2:c.-11-2739C>T
PUM1 transcript variant 2 NM_014676.2:c.-11-2739= NM_014676.2:c.-11-2739C>T
PUM1 transcript variant 2 NM_014676.3:c.-11-2739= NM_014676.3:c.-11-2739C>T
PUM1 transcript variant X1 XM_005271357.1:c.98-2739= XM_005271357.1:c.98-2739C>T
PUM1 transcript variant X2 XM_005271358.1:c.98-2739= XM_005271358.1:c.98-2739C>T
PUM1 transcript variant X3 XM_005271359.1:c.98-2739= XM_005271359.1:c.98-2739C>T
PUM1 transcript variant X4 XM_005271360.1:c.-11-2739= XM_005271360.1:c.-11-2739C>T
PUM1 transcript variant X5 XM_005271361.1:c.98-2739= XM_005271361.1:c.98-2739C>T
PUM1 transcript variant X6 XM_005271362.1:c.-11-2739= XM_005271362.1:c.-11-2739C>T
PUM1 transcript variant X7 XM_005271363.1:c.-11-2739= XM_005271363.1:c.-11-2739C>T
PUM1 transcript variant X8 XM_005271364.1:c.-11-2739= XM_005271364.1:c.-11-2739C>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#.

81 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18262181 Feb 28, 2004 (120)
2 ILLUMINA ss66701250 Dec 01, 2006 (127)
3 ILLUMINA ss66983909 Dec 01, 2006 (127)
4 ILLUMINA ss67157742 Dec 01, 2006 (127)
5 CSHL-HAPMAP ss68365846 Jan 12, 2007 (127)
6 ILLUMINA ss70405262 May 17, 2007 (127)
7 ILLUMINA ss70556470 May 23, 2008 (130)
8 ILLUMINA ss71093857 May 17, 2007 (127)
9 ILLUMINA ss75637094 Dec 07, 2007 (129)
10 HGSV ss78241018 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss85186333 Dec 14, 2007 (130)
12 1000GENOMES ss108098441 Jan 22, 2009 (130)
13 ILLUMINA-UK ss118600773 Feb 14, 2009 (130)
14 ILLUMINA ss121538087 Dec 01, 2009 (131)
15 ILLUMINA ss153136594 Dec 01, 2009 (131)
16 ILLUMINA ss159204696 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss163238433 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss166319896 Jul 04, 2010 (132)
19 ILLUMINA ss170049957 Jul 04, 2010 (132)
20 ILLUMINA ss171877168 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss205369119 Jul 04, 2010 (132)
22 1000GENOMES ss210497156 Jul 14, 2010 (132)
23 1000GENOMES ss218309146 Jul 14, 2010 (132)
24 1000GENOMES ss230480394 Jul 14, 2010 (132)
25 GMI ss284027422 Apr 25, 2013 (138)
26 TISHKOFF ss553947578 Apr 25, 2013 (138)
27 SSMP ss647696772 Apr 25, 2013 (138)
28 ILLUMINA ss825374536 Jul 19, 2016 (147)
29 ILLUMINA ss832717134 Jul 12, 2019 (153)
30 EVA-GONL ss975000184 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1067771407 Aug 21, 2014 (142)
32 1000GENOMES ss1290248402 Aug 21, 2014 (142)
33 DDI ss1425762347 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1573970386 Apr 01, 2015 (144)
35 EVA_DECODE ss1584359816 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1599837329 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1642831362 Apr 01, 2015 (144)
38 EVA_SVP ss1712321700 Apr 01, 2015 (144)
39 WEILL_CORNELL_DGM ss1918212285 Feb 12, 2016 (147)
40 GENOMED ss1966715100 Jul 19, 2016 (147)
41 JJLAB ss2019617651 Sep 14, 2016 (149)
42 USC_VALOUEV ss2147626496 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2161163338 Dec 20, 2016 (150)
44 GNOMAD ss2753291084 Nov 08, 2017 (151)
45 SWEGEN ss2986555039 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023574159 Nov 08, 2017 (151)
47 CSHL ss3343389395 Nov 08, 2017 (151)
48 ILLUMINA ss3637746610 Oct 11, 2018 (152)
49 ILLUMINA ss3638893663 Oct 11, 2018 (152)
50 ILLUMINA ss3639444010 Oct 11, 2018 (152)
51 ILLUMINA ss3642759684 Oct 11, 2018 (152)
52 EGCUT_WGS ss3654618278 Jul 12, 2019 (153)
53 EVA_DECODE ss3686454204 Jul 12, 2019 (153)
54 ACPOP ss3726912990 Jul 12, 2019 (153)
55 EVA ss3746004799 Jul 12, 2019 (153)
56 PACBIO ss3783368329 Jul 12, 2019 (153)
57 PACBIO ss3789034785 Jul 12, 2019 (153)
58 PACBIO ss3793907367 Jul 12, 2019 (153)
59 KHV_HUMAN_GENOMES ss3799022929 Jul 12, 2019 (153)
60 EVA ss3826097162 Apr 25, 2020 (154)
61 EVA ss3836436595 Apr 25, 2020 (154)
62 EVA ss3841841707 Apr 25, 2020 (154)
63 HGDP ss3847328874 Apr 25, 2020 (154)
64 SGDP_PRJ ss3848520850 Apr 25, 2020 (154)
65 KRGDB ss3893460478 Apr 25, 2020 (154)
66 EVA ss3984787086 Apr 25, 2021 (155)
67 EVA ss4016901353 Apr 25, 2021 (155)
68 TOPMED ss4444000242 Apr 25, 2021 (155)
69 TOMMO_GENOMICS ss5143188935 Apr 25, 2021 (155)
70 1000G_HIGH_COVERAGE ss5241702158 Oct 13, 2022 (156)
71 EVA ss5317687561 Oct 13, 2022 (156)
72 HUGCELL_USP ss5442829448 Oct 13, 2022 (156)
73 EVA ss5505803841 Oct 13, 2022 (156)
74 1000G_HIGH_COVERAGE ss5513700600 Oct 13, 2022 (156)
75 SANFORD_IMAGENETICS ss5625217061 Oct 13, 2022 (156)
76 TOMMO_GENOMICS ss5667715956 Oct 13, 2022 (156)
77 YY_MCH ss5800457458 Oct 13, 2022 (156)
78 EVA ss5831743812 Oct 13, 2022 (156)
79 EVA ss5848843327 Oct 13, 2022 (156)
80 EVA ss5907611146 Oct 13, 2022 (156)
81 EVA ss5937034460 Oct 13, 2022 (156)
82 1000Genomes NC_000001.10 - 31535163 Oct 11, 2018 (152)
83 1000Genomes_30x NC_000001.11 - 31062316 Oct 13, 2022 (156)
84 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 31535163 Oct 11, 2018 (152)
85 Genetic variation in the Estonian population NC_000001.10 - 31535163 Oct 11, 2018 (152)
86 The Danish reference pan genome NC_000001.10 - 31535163 Apr 25, 2020 (154)
87 gnomAD - Genomes NC_000001.11 - 31062316 Apr 25, 2021 (155)
88 Genome of the Netherlands Release 5 NC_000001.10 - 31535163 Apr 25, 2020 (154)
89 HGDP-CEPH-db Supplement 1 NC_000001.9 - 31307750 Apr 25, 2020 (154)
90 HapMap NC_000001.11 - 31062316 Apr 25, 2020 (154)
91 KOREAN population from KRGDB NC_000001.10 - 31535163 Apr 25, 2020 (154)
92 Northern Sweden NC_000001.10 - 31535163 Jul 12, 2019 (153)
93 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 31535163 Apr 25, 2021 (155)
94 Qatari NC_000001.10 - 31535163 Apr 25, 2020 (154)
95 SGDP_PRJ NC_000001.10 - 31535163 Apr 25, 2020 (154)
96 Siberian NC_000001.10 - 31535163 Apr 25, 2020 (154)
97 8.3KJPN NC_000001.10 - 31535163 Apr 25, 2021 (155)
98 14KJPN NC_000001.11 - 31062316 Oct 13, 2022 (156)
99 TopMed NC_000001.11 - 31062316 Apr 25, 2021 (155)
100 UK 10K study - Twins NC_000001.10 - 31535163 Oct 11, 2018 (152)
101 ALFA NC_000001.11 - 31062316 Apr 25, 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)
rs56673627 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78241018, ss3638893663, ss3639444010 NC_000001.8:31204255:G:A NC_000001.11:31062315:G:A (self)
6766, ss108098441, ss118600773, ss163238433, ss166319896, ss205369119, ss210497156, ss284027422, ss825374536, ss1584359816, ss1712321700, ss3642759684, ss3847328874 NC_000001.9:31307749:G:A NC_000001.11:31062315:G:A (self)
943881, 505638, 356526, 1444803, 217599, 637872, 197855, 13013, 254215, 537830, 142850, 1158242, 505638, ss218309146, ss230480394, ss553947578, ss647696772, ss832717134, ss975000184, ss1067771407, ss1290248402, ss1425762347, ss1573970386, ss1599837329, ss1642831362, ss1918212285, ss1966715100, ss2019617651, ss2147626496, ss2753291084, ss2986555039, ss3343389395, ss3637746610, ss3654618278, ss3726912990, ss3746004799, ss3783368329, ss3789034785, ss3793907367, ss3826097162, ss3836436595, ss3848520850, ss3893460478, ss3984787086, ss4016901353, ss5143188935, ss5317687561, ss5505803841, ss5625217061, ss5831743812, ss5937034460 NC_000001.10:31535162:G:A NC_000001.11:31062315:G:A (self)
1226535, 6633494, 39615, 1553060, 7606577, 3630573588, ss2161163338, ss3023574159, ss3686454204, ss3799022929, ss3841841707, ss4444000242, ss5241702158, ss5442829448, ss5513700600, ss5667715956, ss5800457458, ss5848843327, ss5907611146 NC_000001.11:31062315:G:A NC_000001.11:31062315:G:A (self)
ss18262181 NT_004511.16:1473564:G:A NC_000001.11:31062315:G:A (self)
ss66701250, ss66983909, ss67157742, ss68365846, ss70405262, ss70556470, ss71093857, ss75637094, ss85186333, ss121538087, ss153136594, ss159204696, ss170049957, ss171877168 NT_032977.9:1507080:G:A NC_000001.11:31062315:G:A (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 rs12126748

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