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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs684047

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:99857027 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.443250 (60860/137304, GnomAD)
C=0.42199 (11922/28252, 14KJPN)
C=0.42887 (7187/16758, 8.3KJPN) (+ 14 more)
T=0.4543 (2275/5008, 1000G)
T=0.4272 (1907/4464, Estonian)
T=0.4920 (1896/3854, ALSPAC)
T=0.4943 (1833/3708, TWINSUK)
A=0.0000 (0/3424, ALFA)
G=0.0000 (0/3424, ALFA)
T=0.0000 (0/3424, ALFA)
C=0.4347 (1272/2926, KOREAN)
C=0.4361 (798/1830, Korea1K)
T=0.493 (295/598, NorthernSweden)
C=0.316 (131/414, SGDP_PRJ)
T=0.384 (83/216, Qatari)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AGL : 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 3424 C=1.0000 A=0.0000, G=0.0000, T=0.0000
European Sub 2128 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Sub 880 C=1.000 A=0.000, G=0.000, T=0.000
African Others Sub 40 C=1.00 A=0.00, G=0.00, T=0.00
African American Sub 840 C=1.000 A=0.000, G=0.000, T=0.000
Asian Sub 32 C=1.00 A=0.00, G=0.00, T=0.00
East Asian Sub 24 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 8 C=1.0 A=0.0, G=0.0, T=0.0
Latin American 1 Sub 46 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 2 Sub 162 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 24 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 152 C=1.000 A=0.000, G=0.000, T=0.000


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
gnomAD - Genomes Global Study-wide 137304 C=0.556750 T=0.443250
gnomAD - Genomes European Sub 74338 C=0.53305 T=0.46695
gnomAD - Genomes African Sub 41186 C=0.60006 T=0.39994
gnomAD - Genomes American Sub 13404 C=0.55431 T=0.44569
gnomAD - Genomes Ashkenazi Jewish Sub 3240 C=0.6222 T=0.3778
gnomAD - Genomes East Asian Sub 3030 C=0.4964 T=0.5036
gnomAD - Genomes Other Sub 2106 C=0.5480 T=0.4520
14KJPN JAPANESE Study-wide 28252 C=0.42199 T=0.57801
8.3KJPN JAPANESE Study-wide 16758 C=0.42887 T=0.57113
1000Genomes Global Study-wide 5008 C=0.5457 T=0.4543
1000Genomes African Sub 1322 C=0.6172 T=0.3828
1000Genomes East Asian Sub 1008 C=0.5010 T=0.4990
1000Genomes Europe Sub 1006 C=0.5507 T=0.4493
1000Genomes South Asian Sub 978 C=0.528 T=0.472
1000Genomes American Sub 694 C=0.493 T=0.507
Genetic variation in the Estonian population Estonian Study-wide 4464 C=0.5728 T=0.4272
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5080 T=0.4920
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5057 T=0.4943
Allele Frequency Aggregator Total Global 3424 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator European Sub 2128 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 880 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 162 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 152 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 46 C=1.00 A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 32 C=1.00 A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 24 C=1.00 A=0.00, G=0.00, T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2926 C=0.4347 G=0.0000, T=0.5653
Korean Genome Project KOREAN Study-wide 1830 C=0.4361 T=0.5639
Northern Sweden ACPOP Study-wide 598 C=0.507 T=0.493
SGDP_PRJ Global Study-wide 414 C=0.316 T=0.684
Qatari Global Study-wide 216 C=0.616 T=0.384
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 1 NC_000001.11:g.99857027C>A
GRCh38.p14 chr 1 NC_000001.11:g.99857027C>G
GRCh38.p14 chr 1 NC_000001.11:g.99857027C>T
GRCh37.p13 chr 1 NC_000001.10:g.100322583C>A
GRCh37.p13 chr 1 NC_000001.10:g.100322583C>G
GRCh37.p13 chr 1 NC_000001.10:g.100322583C>T
AGL RefSeqGene NG_012865.1:g.11944C>A
AGL RefSeqGene NG_012865.1:g.11944C>G
AGL RefSeqGene NG_012865.1:g.11944C>T
Gene: AGL, amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AGL transcript variant 4 NM_000028.2:c.83-4476C>A N/A Intron Variant
AGL transcript variant 1 NM_000642.3:c.83-4476C>A N/A Intron Variant
AGL transcript variant 3 NM_000643.2:c.83-4476C>A N/A Intron Variant
AGL transcript variant 2 NM_000644.2:c.83-4476C>A N/A Intron Variant
AGL transcript variant 6 NM_000646.2:c.34+4324C>A N/A Intron Variant
AGL transcript variant X1 XM_005270557.3:c.83-4476C…

XM_005270557.3:c.83-4476C>A

 		N/A Intron Variant
AGL transcript variant X2 XM_017000501.3:c. N/A Genic 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 C= A G T
GRCh38.p14 chr 1 NC_000001.11:g.99857027= NC_000001.11:g.99857027C>A NC_000001.11:g.99857027C>G NC_000001.11:g.99857027C>T
GRCh37.p13 chr 1 NC_000001.10:g.100322583= NC_000001.10:g.100322583C>A NC_000001.10:g.100322583C>G NC_000001.10:g.100322583C>T
AGL RefSeqGene NG_012865.1:g.11944= NG_012865.1:g.11944C>A NG_012865.1:g.11944C>G NG_012865.1:g.11944C>T
AGL transcript variant 4 NM_000028.2:c.83-4476= NM_000028.2:c.83-4476C>A NM_000028.2:c.83-4476C>G NM_000028.2:c.83-4476C>T
AGL transcript variant 1 NM_000642.2:c.83-4476= NM_000642.2:c.83-4476C>A NM_000642.2:c.83-4476C>G NM_000642.2:c.83-4476C>T
AGL transcript variant 1 NM_000642.3:c.83-4476= NM_000642.3:c.83-4476C>A NM_000642.3:c.83-4476C>G NM_000642.3:c.83-4476C>T
AGL transcript variant 3 NM_000643.2:c.83-4476= NM_000643.2:c.83-4476C>A NM_000643.2:c.83-4476C>G NM_000643.2:c.83-4476C>T
AGL transcript variant 2 NM_000644.2:c.83-4476= NM_000644.2:c.83-4476C>A NM_000644.2:c.83-4476C>G NM_000644.2:c.83-4476C>T
AGL transcript variant 6 NM_000646.2:c.34+4324= NM_000646.2:c.34+4324C>A NM_000646.2:c.34+4324C>G NM_000646.2:c.34+4324C>T
AGL transcript variant X1 XM_005270557.1:c.83-4476= XM_005270557.1:c.83-4476C>A XM_005270557.1:c.83-4476C>G XM_005270557.1:c.83-4476C>T
AGL transcript variant X1 XM_005270557.3:c.83-4476= XM_005270557.3:c.83-4476C>A XM_005270557.3:c.83-4476C>G XM_005270557.3:c.83-4476C>T
AGL transcript variant X2 XM_005270558.1:c.34+4324= XM_005270558.1:c.34+4324C>A XM_005270558.1:c.34+4324C>G XM_005270558.1:c.34+4324C>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#.

47 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15426179 Feb 27, 2004 (124)
2 CSHL-HAPMAP ss16388818 Feb 27, 2004 (124)
3 SC_SNP ss18140549 Feb 27, 2004 (124)
4 SSAHASNP ss20472909 Apr 05, 2004 (124)
5 ENSEMBL ss131629878 Dec 01, 2009 (131)
6 BUSHMAN ss198835607 Jul 04, 2010 (142)
7 GMI ss275946120 May 04, 2012 (137)
8 1000GENOMES ss328807680 May 09, 2011 (134)
9 SSMP ss648255303 Apr 25, 2013 (138)
10 EVA-GONL ss975485275 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1068129246 Aug 21, 2014 (142)
12 1000GENOMES ss1292115111 Aug 21, 2014 (142)
13 DDI ss1425911718 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1600821143 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1643815176 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1918684681 Feb 12, 2016 (147)
17 JJLAB ss2019863984 Sep 14, 2016 (149)
18 USC_VALOUEV ss2147882549 Dec 20, 2016 (150)
19 SYSTEMSBIOZJU ss2624443386 Nov 08, 2017 (151)
20 GRF ss2697810046 Nov 08, 2017 (151)
21 GNOMAD ss2758658917 Nov 08, 2017 (151)
22 SWEGEN ss2987308780 Nov 08, 2017 (151)
23 CSHL ss3343596965 Nov 08, 2017 (151)
24 URBANLAB ss3646732060 Oct 11, 2018 (152)
25 EGCUT_WGS ss3655393958 Jul 12, 2019 (153)
26 EVA_DECODE ss3687371076 Jul 12, 2019 (153)
27 ACPOP ss3727315979 Jul 12, 2019 (153)
28 EVA ss3746576450 Jul 12, 2019 (153)
29 PACBIO ss3783496640 Jul 12, 2019 (153)
30 PACBIO ss3789141578 Jul 12, 2019 (153)
31 PACBIO ss3794014420 Jul 12, 2019 (153)
32 KHV_HUMAN_GENOMES ss3799577300 Jul 12, 2019 (153)
33 EVA ss3836554175 Apr 25, 2020 (154)
34 EVA ss3841962183 Apr 25, 2020 (154)
35 SGDP_PRJ ss3849481655 Apr 25, 2020 (154)
36 KRGDB ss3894559973 Apr 25, 2020 (154)
37 KOGIC ss3945094727 Apr 25, 2020 (154)
38 TOMMO_GENOMICS ss5145321802 Apr 25, 2021 (155)
39 1000G_HIGH_COVERAGE ss5243328215 Oct 12, 2022 (156)
40 EVA ss5320685485 Oct 12, 2022 (156)
41 EVA ss5505965310 Oct 12, 2022 (156)
42 SANFORD_IMAGENETICS ss5626135679 Oct 12, 2022 (156)
43 TOMMO_GENOMICS ss5670483644 Oct 12, 2022 (156)
44 YY_MCH ss5800861533 Oct 12, 2022 (156)
45 EVA ss5832374804 Oct 12, 2022 (156)
46 EVA ss5909480989 Oct 12, 2022 (156)
47 EVA ss5937996925 Oct 12, 2022 (156)
48 1000Genomes NC_000001.10 - 100322583 Oct 11, 2018 (152)
49 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100322583 Oct 11, 2018 (152)
50 Genetic variation in the Estonian population NC_000001.10 - 100322583 Oct 11, 2018 (152)
51 gnomAD - Genomes NC_000001.11 - 99857027 Apr 25, 2021 (155)
52 KOREAN population from KRGDB NC_000001.10 - 100322583 Apr 25, 2020 (154)
53 Korean Genome Project NC_000001.11 - 99857027 Apr 25, 2020 (154)
54 Northern Sweden NC_000001.10 - 100322583 Jul 12, 2019 (153)
55 Qatari NC_000001.10 - 100322583 Apr 25, 2020 (154)
56 SGDP_PRJ NC_000001.10 - 100322583 Apr 25, 2020 (154)
57 Siberian NC_000001.10 - 100322583 Apr 25, 2020 (154)
58 8.3KJPN NC_000001.10 - 100322583 Apr 25, 2021 (155)
59 14KJPN NC_000001.11 - 99857027 Oct 12, 2022 (156)
60 UK 10K study - Twins NC_000001.10 - 100322583 Oct 11, 2018 (152)
61 ALFA NC_000001.11 - 99857027 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)
rs10875272 Dec 02, 2004 (124)
rs112986166 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
12558167843 NC_000001.11:99857026:C:A NC_000001.11:99857026:C:A (self)
1737367, ss3894559973 NC_000001.10:100322582:C:G NC_000001.11:99857026:C:G (self)
12558167843 NC_000001.11:99857026:C:G NC_000001.11:99857026:C:G (self)
ss198835607, ss275946120 NC_000001.9:100095170:C:T NC_000001.11:99857026:C:T (self)
2878952, 1588481, 1132206, 1737367, 600844, 726611, 1498635, 398903, 3291109, 1588481, ss328807680, ss648255303, ss975485275, ss1068129246, ss1292115111, ss1425911718, ss1600821143, ss1643815176, ss1918684681, ss2019863984, ss2147882549, ss2624443386, ss2697810046, ss2758658917, ss2987308780, ss3343596965, ss3655393958, ss3727315979, ss3746576450, ss3783496640, ss3789141578, ss3794014420, ss3836554175, ss3849481655, ss3894559973, ss5145321802, ss5320685485, ss5505965310, ss5626135679, ss5832374804, ss5937996925 NC_000001.10:100322582:C:T NC_000001.11:99857026:C:T (self)
20350861, 1472728, 4320748, 12558167843, ss3646732060, ss3687371076, ss3799577300, ss3841962183, ss3945094727, ss5243328215, ss5670483644, ss5800861533, ss5909480989 NC_000001.11:99857026:C:T NC_000001.11:99857026:C:T (self)
ss15426179, ss16388818, ss18140549, ss20472909 NT_028050.13:8511526:C:T NC_000001.11:99857026:C:T (self)
ss131629878 NT_032977.9:70294500:C:T NC_000001.11:99857026: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 rs684047

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