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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.

rs4680662

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:165798762 (GRCh38.p13) 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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.378027 (100060/264690, TOPMED)
A=0.19857 (3328/16760, 8.3KJPN)
A=0.4010 (3523/8786, ALFA) (+ 14 more)
A=0.3674 (1840/5008, 1000G)
A=0.2330 (1044/4480, Estonian)
A=0.2385 (919/3854, ALSPAC)
A=0.2376 (881/3708, TWINSUK)
A=0.2027 (594/2930, KOREAN)
A=0.2112 (387/1832, Korea1K)
A=0.238 (238/998, GoNL)
A=0.198 (119/600, NorthernSweden)
A=0.242 (111/458, SGDP_PRJ)
A=0.361 (78/216, Qatari)
A=0.167 (36/216, Vietnamese)
A=0.490 (102/208, HapMap)
A=0.22 (11/50, Siberian)
A=0.23 (9/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCHE : Intron Variant
Publications
2 citations
Genomic View
See rs on genome
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.p13 chr 3 NC_000003.12:g.165798762A>C
GRCh38.p13 chr 3 NC_000003.12:g.165798762A>G
GRCh38.p13 chr 3 NC_000003.12:g.165798762A>T
GRCh37.p13 chr 3 NC_000003.11:g.165516550A>C
GRCh37.p13 chr 3 NC_000003.11:g.165516550A>G
GRCh37.p13 chr 3 NC_000003.11:g.165516550A>T
BCHE RefSeqGene NG_009031.1:g.43704T>G
BCHE RefSeqGene NG_009031.1:g.43704T>C
BCHE RefSeqGene NG_009031.1:g.43704T>A
Gene: BCHE, butyrylcholinesterase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BCHE transcript variant 1 NM_000055.4:c.1518-12451T…

NM_000055.4:c.1518-12451T>G

N/A Intron Variant
BCHE transcript variant 2 NR_137635.2:n. N/A Intron Variant
BCHE transcript variant 3 NR_137636.2:n. 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 8786 A=0.4010 C=0.0000, G=0.5990, T=0.0000
European Sub 7148 A=0.2916 C=0.0000, G=0.7084, T=0.0000
African Sub 1246 A=0.9639 C=0.0000, G=0.0361, T=0.0000
African Others Sub 54 A=0.98 C=0.00, G=0.02, T=0.00
African American Sub 1192 A=0.9631 C=0.0000, G=0.0369, T=0.0000
Asian Sub 14 A=0.79 C=0.00, G=0.21, T=0.00
East Asian Sub 6 A=0.7 C=0.0, G=0.3, T=0.0
Other Asian Sub 8 A=0.9 C=0.0, G=0.1, T=0.0
Latin American 1 Sub 24 A=1.00 C=0.00, G=0.00, T=0.00
Latin American 2 Sub 50 A=1.00 C=0.00, G=0.00, T=0.00
South Asian Sub 18 A=0.89 C=0.00, G=0.11, T=0.00
Other Sub 286 A=0.479 C=0.000, G=0.521, 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
TopMed Global Study-wide 264690 A=0.378027 G=0.621973
8.3KJPN JAPANESE Study-wide 16760 A=0.19857 G=0.80143
1000Genomes Global Study-wide 5008 A=0.3674 G=0.6326
1000Genomes African Sub 1322 A=0.6974 G=0.3026
1000Genomes East Asian Sub 1008 A=0.2252 G=0.7748
1000Genomes Europe Sub 1006 A=0.2475 G=0.7525
1000Genomes South Asian Sub 978 A=0.224 G=0.776
1000Genomes American Sub 694 A=0.321 G=0.679
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2330 G=0.7670
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2385 G=0.7615
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2376 G=0.7624
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.2027 C=0.0000, G=0.7973, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.2112 G=0.7888
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.238 G=0.762
Northern Sweden ACPOP Study-wide 600 A=0.198 G=0.802
SGDP_PRJ Global Study-wide 458 A=0.242 G=0.758
Qatari Global Study-wide 216 A=0.361 G=0.639
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.167 G=0.833
HapMap Global Study-wide 208 A=0.490 G=0.510
HapMap African Sub 120 A=0.733 G=0.267
HapMap Asian Sub 88 A=0.16 G=0.84
Siberian Global Study-wide 50 A=0.22 G=0.78
The Danish reference pan genome Danish Study-wide 40 A=0.23 G=0.78
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 T
GRCh38.p13 chr 3 NC_000003.12:g.165798762= NC_000003.12:g.165798762A>C NC_000003.12:g.165798762A>G NC_000003.12:g.165798762A>T
GRCh37.p13 chr 3 NC_000003.11:g.165516550= NC_000003.11:g.165516550A>C NC_000003.11:g.165516550A>G NC_000003.11:g.165516550A>T
BCHE RefSeqGene NG_009031.1:g.43704= NG_009031.1:g.43704T>G NG_009031.1:g.43704T>C NG_009031.1:g.43704T>A
BCHE transcript NM_000055.2:c.1518-12451= NM_000055.2:c.1518-12451T>G NM_000055.2:c.1518-12451T>C NM_000055.2:c.1518-12451T>A
BCHE transcript variant 1 NM_000055.4:c.1518-12451= NM_000055.4:c.1518-12451T>G NM_000055.4:c.1518-12451T>C NM_000055.4:c.1518-12451T>A
BCHE transcript variant X1 XM_005247685.1:c.1641-12451= XM_005247685.1:c.1641-12451T>G XM_005247685.1:c.1641-12451T>C XM_005247685.1:c.1641-12451T>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#.

63 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6445552 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss14187843 Dec 05, 2003 (119)
3 SSAHASNP ss21968101 Apr 05, 2004 (123)
4 ABI ss44459813 Mar 13, 2006 (126)
5 BCMHGSC_JDW ss92361261 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss99148026 Feb 06, 2009 (130)
7 1000GENOMES ss112663399 Jan 25, 2009 (130)
8 ENSEMBL ss135437647 Dec 01, 2009 (131)
9 ENSEMBL ss139277494 Dec 01, 2009 (131)
10 GMI ss156468994 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss167408853 Jul 04, 2010 (132)
12 BUSHMAN ss203479339 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss206017712 Jul 04, 2010 (132)
14 1000GENOMES ss220557109 Jul 14, 2010 (132)
15 1000GENOMES ss232127356 Jul 14, 2010 (132)
16 1000GENOMES ss239478374 Jul 15, 2010 (132)
17 BL ss253661848 May 09, 2011 (134)
18 GMI ss277441771 May 04, 2012 (137)
19 GMI ss284790049 Apr 25, 2013 (138)
20 PJP ss292967602 May 09, 2011 (134)
21 TISHKOFF ss557091685 Apr 25, 2013 (138)
22 SSMP ss650834318 Apr 25, 2013 (138)
23 EVA-GONL ss979412418 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1071021956 Aug 21, 2014 (142)
25 1000GENOMES ss1307113131 Aug 21, 2014 (142)
26 DDI ss1429661239 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1580280640 Apr 01, 2015 (144)
28 EVA_DECODE ss1588906170 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1608719191 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1651713224 Apr 01, 2015 (144)
31 HAMMER_LAB ss1800378450 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1922635016 Feb 12, 2016 (147)
33 GENOMED ss1969580501 Jul 19, 2016 (147)
34 JJLAB ss2021892330 Sep 14, 2016 (149)
35 USC_VALOUEV ss2149988411 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2257823178 Dec 20, 2016 (150)
37 TOPMED ss2425214797 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2625447318 Nov 08, 2017 (151)
39 GRF ss2705408229 Nov 08, 2017 (151)
40 GNOMAD ss2801870629 Nov 08, 2017 (151)
41 SWEGEN ss2993578654 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3024714855 Nov 08, 2017 (151)
43 CSHL ss3345377254 Nov 08, 2017 (151)
44 TOPMED ss3411814337 Nov 08, 2017 (151)
45 TOPMED ss3411814338 Nov 08, 2017 (151)
46 TOPMED ss3411814339 Nov 08, 2017 (151)
47 URBANLAB ss3647578594 Oct 12, 2018 (152)
48 EGCUT_WGS ss3661522436 Jul 13, 2019 (153)
49 EVA_DECODE ss3710749574 Jul 13, 2019 (153)
50 ACPOP ss3730558505 Jul 13, 2019 (153)
51 EVA ss3760987185 Jul 13, 2019 (153)
52 PACBIO ss3784528187 Jul 13, 2019 (153)
53 PACBIO ss3790011880 Jul 13, 2019 (153)
54 PACBIO ss3794886525 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3804121911 Jul 13, 2019 (153)
56 EVA ss3828197037 Apr 25, 2020 (154)
57 EVA ss3837532272 Apr 25, 2020 (154)
58 EVA ss3842964171 Apr 25, 2020 (154)
59 SGDP_PRJ ss3857474637 Apr 25, 2020 (154)
60 KRGDB ss3903537586 Apr 25, 2020 (154)
61 KOGIC ss3952869222 Apr 25, 2020 (154)
62 TOPMED ss4591977325 Apr 26, 2021 (155)
63 TOMMO_GENOMICS ss5162661067 Apr 26, 2021 (155)
64 1000Genomes NC_000003.11 - 165516550 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 165516550 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000003.11 - 165516550 Oct 12, 2018 (152)
67 The Danish reference pan genome NC_000003.11 - 165516550 Apr 25, 2020 (154)
68 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 130800568 (NC_000003.12:165798761:A:C 9/139992)
Row 130800569 (NC_000003.12:165798761:A:G 88864/139916)

- Apr 26, 2021 (155)
69 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 130800568 (NC_000003.12:165798761:A:C 9/139992)
Row 130800569 (NC_000003.12:165798761:A:G 88864/139916)

- Apr 26, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000003.11 - 165516550 Apr 25, 2020 (154)
71 HapMap NC_000003.12 - 165798762 Apr 25, 2020 (154)
72 KOREAN population from KRGDB NC_000003.11 - 165516550 Apr 25, 2020 (154)
73 Korean Genome Project NC_000003.12 - 165798762 Apr 25, 2020 (154)
74 Northern Sweden NC_000003.11 - 165516550 Jul 13, 2019 (153)
75 Qatari NC_000003.11 - 165516550 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000003.11 - 165516550 Apr 25, 2020 (154)
77 Siberian NC_000003.11 - 165516550 Apr 25, 2020 (154)
78 8.3KJPN NC_000003.11 - 165516550 Apr 26, 2021 (155)
79 TopMed NC_000003.12 - 165798762 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000003.11 - 165516550 Oct 12, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000003.11 - 165516550 Jul 13, 2019 (153)
82 ALFA NC_000003.12 - 165798762 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)
rs13084030 Sep 24, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10714980, ss2801870629, ss3903537586 NC_000003.11:165516549:A:C NC_000003.12:165798761:A:C (self)
14479993595, ss2257823178, ss3411814337 NC_000003.12:165798761:A:C NC_000003.12:165798761:A:C (self)
ss92361261, ss112663399, ss167408853, ss203479339, ss206017712, ss253661848, ss277441771, ss284790049, ss292967602, ss1588906170 NC_000003.10:166999243:A:G NC_000003.12:165798761:A:G (self)
18412845, 10257802, 7260684, 6445579, 4507861, 10714980, 3843370, 4676946, 9491617, 2504765, 20630374, 10257802, 2243403, ss220557109, ss232127356, ss239478374, ss557091685, ss650834318, ss979412418, ss1071021956, ss1307113131, ss1429661239, ss1580280640, ss1608719191, ss1651713224, ss1800378450, ss1922635016, ss1969580501, ss2021892330, ss2149988411, ss2425214797, ss2625447318, ss2705408229, ss2801870629, ss2993578654, ss3345377254, ss3661522436, ss3730558505, ss3760987185, ss3784528187, ss3790011880, ss3794886525, ss3828197037, ss3837532272, ss3857474637, ss3903537586, ss5162661067 NC_000003.11:165516549:A:G NC_000003.12:165798761:A:G (self)
2502552, 9247223, 268359135, 429354880, 14479993595, ss2257823178, ss3024714855, ss3411814338, ss3647578594, ss3710749574, ss3804121911, ss3842964171, ss3952869222, ss4591977325 NC_000003.12:165798761:A:G NC_000003.12:165798761:A:G (self)
ss14187843, ss21968101 NT_005612.14:72011707:A:G NC_000003.12:165798761:A:G (self)
ss6445552, ss44459813, ss99148026, ss135437647, ss139277494, ss156468994 NT_005612.16:72011695:A:G NC_000003.12:165798761:A:G (self)
10714980, ss3903537586 NC_000003.11:165516549:A:T NC_000003.12:165798761:A:T (self)
14479993595, ss3411814339 NC_000003.12:165798761:A:T NC_000003.12:165798761:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs4680662
PMID Title Author Year Journal
20529763 Evaluation of candidate genes for cholinesterase activity in farmworkers exposed to organophosphorus pesticides: association of single nucleotide polymorphisms in BCHE. Howard TD et al. 2010 Environmental health perspectives
30349345 Genetic polymorphism analysis of patients with primary hyperhidrosis. Simes BC et al. 2018 Clinical, cosmetic and investigational dermatology
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.post596+ae089ad