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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.

rs655682

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:226573073 (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>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.293132 (77589/264690, TOPMED)
A=0.393067 (54483/138610, ALFA)
A=0.26954 (7616/28256, 14KJPN) (+ 16 more)
A=0.26808 (4493/16760, 8.3KJPN)
A=0.2509 (1607/6404, 1000G_30x)
A=0.2554 (1279/5008, 1000G)
A=0.3533 (1583/4480, Estonian)
A=0.4017 (1548/3854, ALSPAC)
A=0.3908 (1449/3708, TWINSUK)
A=0.2447 (717/2930, KOREAN)
A=0.2643 (500/1892, HapMap)
A=0.2484 (455/1832, Korea1K)
A=0.402 (401/998, GoNL)
A=0.357 (214/600, NorthernSweden)
A=0.208 (104/500, SGDP_PRJ)
G=0.468 (101/216, Qatari)
A=0.241 (52/216, Vietnamese)
A=0.25 (14/56, Siberian)
A=0.47 (19/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STUM : 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 138610 A=0.393067 C=0.000000, G=0.606933
European Sub 121896 A=0.410145 C=0.000000, G=0.589855
African Sub 3936 A=0.1547 C=0.0000, G=0.8453
African Others Sub 134 A=0.052 C=0.000, G=0.948
African American Sub 3802 A=0.1583 C=0.0000, G=0.8417
Asian Sub 530 A=0.287 C=0.000, G=0.713
East Asian Sub 418 A=0.297 C=0.000, G=0.703
Other Asian Sub 112 A=0.250 C=0.000, G=0.750
Latin American 1 Sub 628 A=0.322 C=0.000, G=0.678
Latin American 2 Sub 5744 A=0.2140 C=0.0000, G=0.7860
South Asian Sub 112 A=0.536 C=0.000, G=0.464
Other Sub 5764 A=0.3879 C=0.0000, G=0.6121


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=0.293132 G=0.706868
Allele Frequency Aggregator Total Global 138610 A=0.393067 C=0.000000, G=0.606933
Allele Frequency Aggregator European Sub 121896 A=0.410145 C=0.000000, G=0.589855
Allele Frequency Aggregator Other Sub 5764 A=0.3879 C=0.0000, G=0.6121
Allele Frequency Aggregator Latin American 2 Sub 5744 A=0.2140 C=0.0000, G=0.7860
Allele Frequency Aggregator African Sub 3936 A=0.1547 C=0.0000, G=0.8453
Allele Frequency Aggregator Latin American 1 Sub 628 A=0.322 C=0.000, G=0.678
Allele Frequency Aggregator Asian Sub 530 A=0.287 C=0.000, G=0.713
Allele Frequency Aggregator South Asian Sub 112 A=0.536 C=0.000, G=0.464
14KJPN JAPANESE Study-wide 28256 A=0.26954 G=0.73046
8.3KJPN JAPANESE Study-wide 16760 A=0.26808 G=0.73192
1000Genomes_30x Global Study-wide 6404 A=0.2509 G=0.7491
1000Genomes_30x African Sub 1786 A=0.1069 G=0.8931
1000Genomes_30x Europe Sub 1266 A=0.3997 G=0.6003
1000Genomes_30x South Asian Sub 1202 A=0.2912 G=0.7088
1000Genomes_30x East Asian Sub 1170 A=0.2872 G=0.7128
1000Genomes_30x American Sub 980 A=0.229 G=0.771
1000Genomes Global Study-wide 5008 A=0.2554 G=0.7446
1000Genomes African Sub 1322 A=0.1036 G=0.8964
1000Genomes East Asian Sub 1008 A=0.2857 G=0.7143
1000Genomes Europe Sub 1006 A=0.4095 G=0.5905
1000Genomes South Asian Sub 978 A=0.292 G=0.708
1000Genomes American Sub 694 A=0.225 G=0.775
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.3533 G=0.6467
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4017 G=0.5983
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3908 G=0.6092
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.2447 G=0.7553
HapMap Global Study-wide 1892 A=0.2643 G=0.7357
HapMap American Sub 770 A=0.305 G=0.695
HapMap African Sub 692 A=0.160 G=0.840
HapMap Asian Sub 254 A=0.252 G=0.748
HapMap Europe Sub 176 A=0.511 G=0.489
Korean Genome Project KOREAN Study-wide 1832 A=0.2484 G=0.7516
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.402 G=0.598
Northern Sweden ACPOP Study-wide 600 A=0.357 G=0.643
SGDP_PRJ Global Study-wide 500 A=0.208 G=0.792
Qatari Global Study-wide 216 A=0.532 G=0.468
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.241 G=0.759
Siberian Global Study-wide 56 A=0.25 G=0.75
The Danish reference pan genome Danish Study-wide 40 A=0.47 G=0.53
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.226573073A>C
GRCh38.p14 chr 1 NC_000001.11:g.226573073A>G
GRCh37.p13 chr 1 NC_000001.10:g.226760774A>C
GRCh37.p13 chr 1 NC_000001.10:g.226760774A>G
Gene: STUM, stum, mechanosensory transduction mediator homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
STUM transcript variant 1 NM_001003665.4:c.203-2372…

NM_001003665.4:c.203-23729A>C

N/A Intron Variant
STUM transcript variant X1 XM_011544183.4:c.203-2372…

XM_011544183.4:c.203-23729A>C

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 A= C G
GRCh38.p14 chr 1 NC_000001.11:g.226573073= NC_000001.11:g.226573073A>C NC_000001.11:g.226573073A>G
GRCh37.p13 chr 1 NC_000001.10:g.226760774= NC_000001.10:g.226760774A>C NC_000001.10:g.226760774A>G
STUM transcript NM_001003665.3:c.203-23729= NM_001003665.3:c.203-23729A>C NM_001003665.3:c.203-23729A>G
STUM transcript variant 1 NM_001003665.4:c.203-23729= NM_001003665.4:c.203-23729A>C NM_001003665.4:c.203-23729A>G
STUM transcript variant X1 XM_011544183.4:c.203-23729= XM_011544183.4:c.203-23729A>C XM_011544183.4:c.203-23729A>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#.

110 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss828731 Aug 11, 2000 (83)
2 KWOK ss2030665 Oct 18, 2000 (87)
3 KWOK ss2031118 Oct 18, 2000 (87)
4 WI_SSAHASNP ss6404382 Feb 20, 2003 (111)
5 CSHL-HAPMAP ss19101430 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss19834100 Feb 27, 2004 (120)
7 SSAHASNP ss20505482 Apr 05, 2004 (121)
8 ABI ss43846759 Mar 13, 2006 (126)
9 PERLEGEN ss68795112 May 17, 2007 (127)
10 ILLUMINA ss75122344 Dec 06, 2007 (129)
11 HGSV ss78340776 Dec 06, 2007 (129)
12 KRIBB_YJKIM ss81431275 Dec 15, 2007 (130)
13 HGSV ss83589998 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss87994051 Mar 23, 2008 (129)
15 HUMANGENOME_JCVI ss99292714 Feb 05, 2009 (130)
16 BGI ss106636633 Feb 05, 2009 (130)
17 1000GENOMES ss109000230 Jan 23, 2009 (130)
18 1000GENOMES ss111870956 Jan 25, 2009 (130)
19 ILLUMINA-UK ss119230137 Feb 15, 2009 (130)
20 ENSEMBL ss138165950 Dec 01, 2009 (131)
21 ENSEMBL ss139048494 Dec 01, 2009 (131)
22 GMI ss156366473 Dec 01, 2009 (131)
23 ILLUMINA ss160786575 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss165861753 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss167544444 Jul 04, 2010 (132)
26 ILLUMINA ss174034041 Jul 04, 2010 (132)
27 BUSHMAN ss199690545 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss205331507 Jul 04, 2010 (132)
29 1000GENOMES ss218916783 Jul 14, 2010 (132)
30 1000GENOMES ss230929434 Jul 14, 2010 (132)
31 1000GENOMES ss238537151 Jul 15, 2010 (132)
32 BL ss253868689 May 09, 2011 (134)
33 GMI ss276244721 May 04, 2012 (137)
34 GMI ss284240928 Apr 25, 2013 (138)
35 PJP ss290747557 May 09, 2011 (134)
36 ILLUMINA ss481282044 May 04, 2012 (137)
37 ILLUMINA ss481306731 May 04, 2012 (137)
38 ILLUMINA ss482289669 Sep 08, 2015 (146)
39 ILLUMINA ss485436270 May 04, 2012 (137)
40 ILLUMINA ss537364235 Sep 08, 2015 (146)
41 TISHKOFF ss555179780 Apr 25, 2013 (138)
42 SSMP ss648751538 Apr 25, 2013 (138)
43 ILLUMINA ss778944086 Sep 08, 2015 (146)
44 ILLUMINA ss783163596 Sep 08, 2015 (146)
45 ILLUMINA ss784119307 Sep 08, 2015 (146)
46 ILLUMINA ss832423008 Sep 08, 2015 (146)
47 ILLUMINA ss834405842 Sep 08, 2015 (146)
48 EVA-GONL ss976215180 Aug 21, 2014 (142)
49 JMKIDD_LAB ss1068654985 Aug 21, 2014 (142)
50 1000GENOMES ss1294917093 Aug 21, 2014 (142)
51 DDI ss1426131926 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1574722848 Apr 01, 2015 (144)
53 EVA_DECODE ss1585613049 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1602282341 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1645276374 Apr 01, 2015 (144)
56 EVA_SVP ss1712410550 Apr 01, 2015 (144)
57 ILLUMINA ss1751902391 Sep 08, 2015 (146)
58 HAMMER_LAB ss1795820111 Sep 08, 2015 (146)
59 WEILL_CORNELL_DGM ss1919437081 Feb 12, 2016 (147)
60 GENOMED ss1966989663 Jul 19, 2016 (147)
61 JJLAB ss2020243063 Sep 14, 2016 (149)
62 USC_VALOUEV ss2148277525 Dec 20, 2016 (150)
63 HUMAN_LONGEVITY ss2170639990 Dec 20, 2016 (150)
64 SYSTEMSBIOZJU ss2624632910 Nov 08, 2017 (151)
65 ILLUMINA ss2632637823 Nov 08, 2017 (151)
66 GRF ss2698275710 Nov 08, 2017 (151)
67 GNOMAD ss2766979557 Nov 08, 2017 (151)
68 SWEGEN ss2988561481 Nov 08, 2017 (151)
69 BIOINF_KMB_FNS_UNIBA ss3023881998 Nov 08, 2017 (151)
70 CSHL ss3343943589 Nov 08, 2017 (151)
71 ILLUMINA ss3626323708 Oct 11, 2018 (152)
72 ILLUMINA ss3630667214 Oct 11, 2018 (152)
73 ILLUMINA ss3632927965 Oct 11, 2018 (152)
74 ILLUMINA ss3633624103 Oct 11, 2018 (152)
75 ILLUMINA ss3634376249 Oct 11, 2018 (152)
76 ILLUMINA ss3635317152 Oct 11, 2018 (152)
77 ILLUMINA ss3636055134 Oct 11, 2018 (152)
78 ILLUMINA ss3637067703 Oct 11, 2018 (152)
79 ILLUMINA ss3637817999 Oct 11, 2018 (152)
80 ILLUMINA ss3640083602 Oct 11, 2018 (152)
81 ILLUMINA ss3642824076 Oct 11, 2018 (152)
82 URBANLAB ss3646901912 Oct 11, 2018 (152)
83 EGCUT_WGS ss3656520617 Jul 12, 2019 (153)
84 EVA_DECODE ss3688761014 Jul 12, 2019 (153)
85 ACPOP ss3727921146 Jul 12, 2019 (153)
86 ILLUMINA ss3744677102 Jul 12, 2019 (153)
87 EVA ss3747419175 Jul 12, 2019 (153)
88 ILLUMINA ss3772177994 Jul 12, 2019 (153)
89 KHV_HUMAN_GENOMES ss3800421859 Jul 12, 2019 (153)
90 EVA ss3826678756 Apr 25, 2020 (154)
91 EVA ss3836741504 Apr 25, 2020 (154)
92 EVA ss3842153775 Apr 25, 2020 (154)
93 SGDP_PRJ ss3851037193 Apr 25, 2020 (154)
94 KRGDB ss3896374726 Apr 25, 2020 (154)
95 KOGIC ss3946629646 Apr 25, 2020 (154)
96 TOPMED ss4485941553 Apr 25, 2021 (155)
97 TOMMO_GENOMICS ss5148740809 Apr 25, 2021 (155)
98 1000G_HIGH_COVERAGE ss5246030092 Oct 12, 2022 (156)
99 EVA ss5314687541 Oct 12, 2022 (156)
100 EVA ss5325217592 Oct 12, 2022 (156)
101 HUGCELL_USP ss5446441926 Oct 12, 2022 (156)
102 1000G_HIGH_COVERAGE ss5520246384 Oct 12, 2022 (156)
103 SANFORD_IMAGENETICS ss5627579583 Oct 12, 2022 (156)
104 TOMMO_GENOMICS ss5676589098 Oct 12, 2022 (156)
105 EVA ss5799513735 Oct 12, 2022 (156)
106 YY_MCH ss5801698756 Oct 12, 2022 (156)
107 EVA ss5833356811 Oct 12, 2022 (156)
108 EVA ss5849315458 Oct 12, 2022 (156)
109 EVA ss5912241548 Oct 12, 2022 (156)
110 EVA ss5939423912 Oct 12, 2022 (156)
111 1000Genomes NC_000001.10 - 226760774 Oct 11, 2018 (152)
112 1000Genomes_30x NC_000001.11 - 226573073 Oct 12, 2022 (156)
113 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 226760774 Oct 11, 2018 (152)
114 Genetic variation in the Estonian population NC_000001.10 - 226760774 Oct 11, 2018 (152)
115 The Danish reference pan genome NC_000001.10 - 226760774 Apr 25, 2020 (154)
116 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 41522201 (NC_000001.11:226573072:A:C 2/140110)
Row 41522202 (NC_000001.11:226573072:A:G 97118/140058)

- Apr 25, 2021 (155)
117 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 41522201 (NC_000001.11:226573072:A:C 2/140110)
Row 41522202 (NC_000001.11:226573072:A:G 97118/140058)

- Apr 25, 2021 (155)
118 Genome of the Netherlands Release 5 NC_000001.10 - 226760774 Apr 25, 2020 (154)
119 HapMap NC_000001.11 - 226573073 Apr 25, 2020 (154)
120 KOREAN population from KRGDB NC_000001.10 - 226760774 Apr 25, 2020 (154)
121 Korean Genome Project NC_000001.11 - 226573073 Apr 25, 2020 (154)
122 Northern Sweden NC_000001.10 - 226760774 Jul 12, 2019 (153)
123 Qatari NC_000001.10 - 226760774 Apr 25, 2020 (154)
124 SGDP_PRJ NC_000001.10 - 226760774 Apr 25, 2020 (154)
125 Siberian NC_000001.10 - 226760774 Apr 25, 2020 (154)
126 8.3KJPN NC_000001.10 - 226760774 Apr 25, 2021 (155)
127 14KJPN NC_000001.11 - 226573073 Oct 12, 2022 (156)
128 TopMed NC_000001.11 - 226573073 Apr 25, 2021 (155)
129 UK 10K study - Twins NC_000001.10 - 226760774 Oct 11, 2018 (152)
130 A Vietnamese Genetic Variation Database NC_000001.10 - 226760774 Jul 12, 2019 (153)
131 ALFA NC_000001.11 - 226573073 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)
rs59116646 May 25, 2008 (130)
rs59360679 Feb 26, 2009 (130)
rs111181703 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
558049404 NC_000001.11:226573072:A:C NC_000001.11:226573072:A:C (self)
ss78340776, ss83589998 NC_000001.8:223067508:A:G NC_000001.11:226573072:A:G (self)
ss87994051, ss109000230, ss111870956, ss119230137, ss165861753, ss167544444, ss199690545, ss205331507, ss253868689, ss276244721, ss284240928, ss290747557, ss481282044, ss1585613049, ss1712410550, ss3642824076 NC_000001.9:224827396:A:G NC_000001.11:226573072:A:G (self)
5781344, 3195487, 2258865, 1913707, 1396477, 3552120, 1206011, 1479011, 3054173, 793879, 6710116, 3195487, 694061, ss218916783, ss230929434, ss238537151, ss481306731, ss482289669, ss485436270, ss537364235, ss555179780, ss648751538, ss778944086, ss783163596, ss784119307, ss832423008, ss834405842, ss976215180, ss1068654985, ss1294917093, ss1426131926, ss1574722848, ss1602282341, ss1645276374, ss1751902391, ss1795820111, ss1919437081, ss1966989663, ss2020243063, ss2148277525, ss2624632910, ss2632637823, ss2698275710, ss2766979557, ss2988561481, ss3343943589, ss3626323708, ss3630667214, ss3632927965, ss3633624103, ss3634376249, ss3635317152, ss3636055134, ss3637067703, ss3637817999, ss3640083602, ss3656520617, ss3727921146, ss3744677102, ss3747419175, ss3772177994, ss3826678756, ss3836741504, ss3851037193, ss3896374726, ss5148740809, ss5314687541, ss5325217592, ss5627579583, ss5799513735, ss5833356811, ss5939423912 NC_000001.10:226760773:A:G NC_000001.11:226573072:A:G (self)
7772319, 282474, 3007647, 10426202, 49547888, 558049404, ss2170639990, ss3023881998, ss3646901912, ss3688761014, ss3800421859, ss3842153775, ss3946629646, ss4485941553, ss5246030092, ss5446441926, ss5520246384, ss5676589098, ss5801698756, ss5849315458, ss5912241548 NC_000001.11:226573072:A:G NC_000001.11:226573072:A:G (self)
ss19101430, ss19834100, ss20505482 NT_004559.11:2936967:A:G NC_000001.11:226573072:A:G (self)
ss828731, ss2030665, ss2031118, ss6404382, ss43846759, ss68795112, ss75122344, ss81431275, ss99292714, ss106636633, ss138165950, ss139048494, ss156366473, ss160786575, ss174034041 NT_167186.1:20278552:A:G NC_000001.11:226573072: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 rs655682

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