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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.

rs12744547

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:15735883 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.220987 (58493/264690, TOPMED)
G=0.225017 (31465/139834, GnomAD)
G=0.05846 (1652/28258, 14KJPN) (+ 15 more)
G=0.23139 (6285/27162, ALFA)
G=0.05692 (954/16760, 8.3KJPN)
G=0.1844 (1181/6404, 1000G_30x)
G=0.1817 (910/5008, 1000G)
G=0.2002 (897/4480, Estonian)
G=0.2250 (867/3854, ALSPAC)
G=0.2268 (841/3708, TWINSUK)
G=0.0503 (147/2922, KOREAN)
G=0.2045 (387/1892, HapMap)
G=0.251 (250/998, GoNL)
G=0.193 (116/600, NorthernSweden)
G=0.292 (63/216, Qatari)
A=0.414 (87/210, SGDP_PRJ)
G=0.25 (10/40, GENOME_DK)
A=0.39 (7/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC25A34 : 2KB Upstream 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 27162 A=0.76861 G=0.23139
European Sub 18124 A=0.77731 G=0.22269
African Sub 7102 A=0.7394 G=0.2606
African Others Sub 230 A=0.778 G=0.222
African American Sub 6872 A=0.7381 G=0.2619
Asian Sub 120 A=0.975 G=0.025
East Asian Sub 94 A=0.97 G=0.03
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 160 A=0.819 G=0.181
Latin American 2 Sub 664 A=0.776 G=0.224
South Asian Sub 98 A=0.77 G=0.23
Other Sub 894 A=0.783 G=0.217


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 A=0.779013 G=0.220987
gnomAD - Genomes Global Study-wide 139834 A=0.774983 G=0.225017
gnomAD - Genomes European Sub 75766 A=0.77918 G=0.22082
gnomAD - Genomes African Sub 41854 A=0.74552 G=0.25448
gnomAD - Genomes American Sub 13622 A=0.80399 G=0.19601
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.7551 G=0.2449
gnomAD - Genomes East Asian Sub 3128 A=0.9552 G=0.0448
gnomAD - Genomes Other Sub 2144 A=0.7854 G=0.2146
14KJPN JAPANESE Study-wide 28258 A=0.94154 G=0.05846
Allele Frequency Aggregator Total Global 27162 A=0.76861 G=0.23139
Allele Frequency Aggregator European Sub 18124 A=0.77731 G=0.22269
Allele Frequency Aggregator African Sub 7102 A=0.7394 G=0.2606
Allele Frequency Aggregator Other Sub 894 A=0.783 G=0.217
Allele Frequency Aggregator Latin American 2 Sub 664 A=0.776 G=0.224
Allele Frequency Aggregator Latin American 1 Sub 160 A=0.819 G=0.181
Allele Frequency Aggregator Asian Sub 120 A=0.975 G=0.025
Allele Frequency Aggregator South Asian Sub 98 A=0.77 G=0.23
8.3KJPN JAPANESE Study-wide 16760 A=0.94308 G=0.05692
1000Genomes_30x Global Study-wide 6404 A=0.8156 G=0.1844
1000Genomes_30x African Sub 1786 A=0.7514 G=0.2486
1000Genomes_30x Europe Sub 1266 A=0.7875 G=0.2125
1000Genomes_30x South Asian Sub 1202 A=0.8319 G=0.1681
1000Genomes_30x East Asian Sub 1170 A=0.9564 G=0.0436
1000Genomes_30x American Sub 980 A=0.781 G=0.219
1000Genomes Global Study-wide 5008 A=0.8183 G=0.1817
1000Genomes African Sub 1322 A=0.7421 G=0.2579
1000Genomes East Asian Sub 1008 A=0.9554 G=0.0446
1000Genomes Europe Sub 1006 A=0.7893 G=0.2107
1000Genomes South Asian Sub 978 A=0.832 G=0.168
1000Genomes American Sub 694 A=0.787 G=0.213
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7998 G=0.2002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7750 G=0.2250
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7732 G=0.2268
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9497 G=0.0503
HapMap Global Study-wide 1892 A=0.7955 G=0.2045
HapMap American Sub 770 A=0.821 G=0.179
HapMap African Sub 692 A=0.704 G=0.296
HapMap Asian Sub 254 A=0.957 G=0.043
HapMap Europe Sub 176 A=0.812 G=0.188
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.749 G=0.251
Northern Sweden ACPOP Study-wide 600 A=0.807 G=0.193
Qatari Global Study-wide 216 A=0.708 G=0.292
SGDP_PRJ Global Study-wide 210 A=0.414 G=0.586
The Danish reference pan genome Danish Study-wide 40 A=0.75 G=0.25
Siberian Global Study-wide 18 A=0.39 G=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.15735883A>G
GRCh37.p13 chr 1 NC_000001.10:g.16062378A>G
PLEKHM2 RefSeqGene NG_053033.1:g.59378A>G
Gene: SLC25A34, solute carrier family 25 member 34 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC25A34 transcript NM_207348.3:c. N/A Upstream Transcript Variant
SLC25A34 transcript variant X2 XM_011541293.2:c. N/A Upstream Transcript Variant
SLC25A34 transcript variant X1 XM_017001083.2:c. N/A Upstream Transcript 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 A= G
GRCh38.p14 chr 1 NC_000001.11:g.15735883= NC_000001.11:g.15735883A>G
GRCh37.p13 chr 1 NC_000001.10:g.16062378= NC_000001.10:g.16062378A>G
PLEKHM2 RefSeqGene NG_053033.1:g.59378= NG_053033.1:g.59378A>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#.

77 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss20534511 Apr 05, 2004 (121)
2 ABI ss43973726 Mar 14, 2006 (126)
3 ILLUMINA ss75027930 Dec 06, 2007 (129)
4 HUMANGENOME_JCVI ss99188921 Feb 04, 2009 (130)
5 ILLUMINA-UK ss118520617 Feb 14, 2009 (130)
6 KRIBB_YJKIM ss119809396 Dec 01, 2009 (131)
7 ENSEMBL ss139196119 Dec 01, 2009 (131)
8 GMI ss154679649 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss163873253 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss166143302 Jul 04, 2010 (132)
11 ILLUMINA ss172237665 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss205343055 Jul 04, 2010 (132)
13 1000GENOMES ss210474123 Jul 14, 2010 (132)
14 1000GENOMES ss218253437 Jul 14, 2010 (132)
15 1000GENOMES ss230439165 Jul 14, 2010 (132)
16 1000GENOMES ss238152291 Jul 15, 2010 (132)
17 BL ss252938184 May 09, 2011 (134)
18 GMI ss275728089 May 04, 2012 (137)
19 ILLUMINA ss410901978 Sep 17, 2011 (135)
20 TISHKOFF ss553830796 Apr 25, 2013 (138)
21 SSMP ss647599545 Apr 25, 2013 (138)
22 EVA-GONL ss974889319 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1067693944 Aug 21, 2014 (142)
24 1000GENOMES ss1289811768 Aug 21, 2014 (142)
25 DDI ss1425723986 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1573906838 Apr 01, 2015 (144)
27 EVA_DECODE ss1584246519 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1599613184 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1642607217 Apr 01, 2015 (144)
30 EVA_SVP ss1712313610 Apr 01, 2015 (144)
31 HAMMER_LAB ss1793963163 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1918092585 Feb 12, 2016 (147)
33 JJLAB ss2019559931 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147559152 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2160295331 Dec 20, 2016 (150)
36 GRF ss2697460336 Nov 08, 2017 (151)
37 GNOMAD ss2751999103 Nov 08, 2017 (151)
38 SWEGEN ss2986360507 Nov 08, 2017 (151)
39 ILLUMINA ss3021058101 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3023544143 Nov 08, 2017 (151)
41 CSHL ss3343335014 Nov 08, 2017 (151)
42 ILLUMINA ss3637739347 Oct 11, 2018 (152)
43 ILLUMINA ss3640975486 Oct 11, 2018 (152)
44 ILLUMINA ss3641269344 Oct 11, 2018 (152)
45 ILLUMINA ss3642753014 Oct 11, 2018 (152)
46 URBANLAB ss3646607776 Oct 11, 2018 (152)
47 ILLUMINA ss3651382305 Oct 11, 2018 (152)
48 EGCUT_WGS ss3654447802 Jul 12, 2019 (153)
49 EVA_DECODE ss3686230366 Jul 12, 2019 (153)
50 ILLUMINA ss3724999613 Jul 12, 2019 (153)
51 ACPOP ss3726820229 Jul 12, 2019 (153)
52 EVA ss3745870189 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3798891383 Jul 12, 2019 (153)
54 EVA ss3826040088 Apr 25, 2020 (154)
55 EVA ss3836407454 Apr 25, 2020 (154)
56 EVA ss3841811662 Apr 25, 2020 (154)
57 SGDP_PRJ ss3848277507 Apr 25, 2020 (154)
58 KRGDB ss3893171085 Apr 25, 2020 (154)
59 EVA ss4016895116 Apr 27, 2021 (155)
60 TOPMED ss4440293649 Apr 27, 2021 (155)
61 TOMMO_GENOMICS ss5142642680 Apr 27, 2021 (155)
62 EVA ss5237260780 Apr 27, 2021 (155)
63 1000G_HIGH_COVERAGE ss5241303918 Oct 17, 2022 (156)
64 EVA ss5316969947 Oct 17, 2022 (156)
65 HUGCELL_USP ss5442483598 Oct 17, 2022 (156)
66 EVA ss5505773697 Oct 17, 2022 (156)
67 1000G_HIGH_COVERAGE ss5513118137 Oct 17, 2022 (156)
68 SANFORD_IMAGENETICS ss5624197613 Oct 17, 2022 (156)
69 SANFORD_IMAGENETICS ss5624997097 Oct 17, 2022 (156)
70 TOMMO_GENOMICS ss5667001496 Oct 17, 2022 (156)
71 YY_MCH ss5800357901 Oct 17, 2022 (156)
72 EVA ss5831585686 Oct 17, 2022 (156)
73 EVA ss5847526896 Oct 17, 2022 (156)
74 EVA ss5848798696 Oct 17, 2022 (156)
75 EVA ss5907173163 Oct 17, 2022 (156)
76 EVA ss5936817173 Oct 17, 2022 (156)
77 EVA ss5979264323 Oct 17, 2022 (156)
78 1000Genomes NC_000001.10 - 16062378 Oct 11, 2018 (152)
79 1000Genomes_30x NC_000001.11 - 15735883 Oct 17, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 16062378 Oct 11, 2018 (152)
81 Genetic variation in the Estonian population NC_000001.10 - 16062378 Oct 11, 2018 (152)
82 The Danish reference pan genome NC_000001.10 - 16062378 Apr 25, 2020 (154)
83 gnomAD - Genomes NC_000001.11 - 15735883 Apr 27, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000001.10 - 16062378 Apr 25, 2020 (154)
85 HapMap NC_000001.11 - 15735883 Apr 25, 2020 (154)
86 KOREAN population from KRGDB NC_000001.10 - 16062378 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 16062378 Jul 12, 2019 (153)
88 Qatari NC_000001.10 - 16062378 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 16062378 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 16062378 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 16062378 Apr 27, 2021 (155)
92 14KJPN NC_000001.11 - 15735883 Oct 17, 2022 (156)
93 TopMed NC_000001.11 - 15735883 Apr 27, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 16062378 Oct 11, 2018 (152)
95 ALFA NC_000001.11 - 15735883 Apr 27, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118520617, ss163873253, ss166143302, ss205343055, ss210474123, ss252938184, ss275728089, ss1584246519, ss1712313610, ss3642753014 NC_000001.9:15934964:A:G NC_000001.11:15735882:A:G (self)
492344, 258233, 186050, 1403130, 112060, 348479, 105094, 134515, 294487, 75506, 611987, 258233, ss218253437, ss230439165, ss238152291, ss553830796, ss647599545, ss974889319, ss1067693944, ss1289811768, ss1425723986, ss1573906838, ss1599613184, ss1642607217, ss1793963163, ss1918092585, ss2019559931, ss2147559152, ss2697460336, ss2751999103, ss2986360507, ss3021058101, ss3343335014, ss3637739347, ss3640975486, ss3641269344, ss3651382305, ss3654447802, ss3726820229, ss3745870189, ss3826040088, ss3836407454, ss3848277507, ss3893171085, ss4016895116, ss5142642680, ss5237260780, ss5316969947, ss5505773697, ss5624197613, ss5624997097, ss5831585686, ss5847526896, ss5936817173, ss5979264323 NC_000001.10:16062377:A:G NC_000001.11:15735882:A:G (self)
644072, 3434669, 19308, 838600, 3899984, 1985062455, ss2160295331, ss3023544143, ss3646607776, ss3686230366, ss3724999613, ss3798891383, ss3841811662, ss4440293649, ss5241303918, ss5442483598, ss5513118137, ss5667001496, ss5800357901, ss5848798696, ss5907173163 NC_000001.11:15735882:A:G NC_000001.11:15735882:A:G (self)
ss43973726, ss75027930, ss99188921, ss119809396, ss139196119, ss154679649, ss172237665, ss410901978 NT_004610.19:2742465:A:G NC_000001.11:15735882:A:G (self)
ss20534511 NT_004873.15:2439542:A:G NC_000001.11:15735882:A:G (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 rs12744547

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