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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.

rs56229264

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:27463672 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.012127 (3210/264690, TOPMED)
A=0.014285 (3592/251444, GnomAD_exome)
A=0.012567 (1762/140206, GnomAD) (+ 16 more)
A=0.013947 (1693/121390, ExAC)
A=0.01986 (1683/84762, ALFA)
A=0.01338 (174/13006, GO-ESP)
A=0.0060 (30/5008, 1000G)
A=0.0237 (106/4480, Estonian)
A=0.0158 (61/3854, ALSPAC)
A=0.0143 (53/3708, TWINSUK)
A=0.021 (21/998, GoNL)
A=0.022 (13/600, NorthernSweden)
A=0.030 (16/534, MGP)
A=0.010 (3/304, FINRISK)
A=0.019 (4/216, Qatari)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNA2 : Synonymous Variant
Publications
0 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 8 NC_000008.11:g.27463672G>A
GRCh37.p13 chr 8 NC_000008.10:g.27321189G>A
CHRNA2 RefSeqGene NG_015827.1:g.20625C>T
Gene: CHRNA2, cholinergic receptor nicotinic alpha 2 subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNA2 transcript variant 1 NM_000742.4:c.771C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Tyr257= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant 3 NM_001347705.2:c.294C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Tyr98= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant 6 NM_001347708.2:c.177C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Tyr59= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant 5 NM_001347707.2:c.177C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Tyr59= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant 4 NM_001347706.2:c.294C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Tyr98= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.726C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Tyr242= Y (Tyr) > Y (Tyr) Synonymous Variant
CHRNA2 transcript variant X1 XM_011544389.2:c.177C>T Y [TAC] > Y [TAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Tyr59= Y (Tyr) > Y (Tyr) Synonymous 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.

Allele: A (allele ID: 134190 )
ClinVar Accession Disease Names Clinical Significance
RCV000116714.2 not specified Likely-Benign
RCV000369041.2 Epilepsy, nocturnal frontal lobe, type 4 Benign
RCV000460445.3 Autosomal dominant nocturnal frontal lobe epilepsy Benign
RCV000716400.1 Seizures Benign

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 84762 G=0.98014 A=0.01986
European Sub 71992 G=0.97896 A=0.02104
African Sub 3630 G=0.9945 A=0.0055
African Others Sub 124 G=1.000 A=0.000
African American Sub 3506 G=0.9943 A=0.0057
Asian Sub 168 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 500 G=0.994 A=0.006
Latin American 2 Sub 648 G=0.989 A=0.011
South Asian Sub 98 G=0.99 A=0.01
Other Sub 7726 G=0.9823 A=0.0177


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=0.987873 A=0.012127
gnomAD - Exomes Global Study-wide 251444 G=0.985715 A=0.014285
gnomAD - Exomes European Sub 135372 G=0.980698 A=0.019302
gnomAD - Exomes Asian Sub 49010 G=0.99484 A=0.00516
gnomAD - Exomes American Sub 34592 G=0.98904 A=0.01096
gnomAD - Exomes African Sub 16256 G=0.99711 A=0.00289
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=0.98125 A=0.01875
gnomAD - Exomes Other Sub 6136 G=0.9819 A=0.0181
gnomAD - Genomes Global Study-wide 140206 G=0.987433 A=0.012567
gnomAD - Genomes European Sub 75938 G=0.98154 A=0.01846
gnomAD - Genomes African Sub 42018 G=0.99710 A=0.00290
gnomAD - Genomes American Sub 13650 G=0.99011 A=0.00989
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9777 A=0.0223
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9865 A=0.0135
ExAC Global Study-wide 121390 G=0.986053 A=0.013947
ExAC Europe Sub 73334 G=0.98070 A=0.01930
ExAC Asian Sub 25166 G=0.99483 A=0.00517
ExAC American Sub 11578 G=0.99093 A=0.00907
ExAC African Sub 10406 G=0.99683 A=0.00317
ExAC Other Sub 906 G=0.989 A=0.011
GO Exome Sequencing Project Global Study-wide 13006 G=0.98662 A=0.01338
GO Exome Sequencing Project European American Sub 8600 G=0.9817 A=0.0183
GO Exome Sequencing Project African American Sub 4406 G=0.9961 A=0.0039
1000Genomes Global Study-wide 5008 G=0.9940 A=0.0060
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9841 A=0.0159
1000Genomes South Asian Sub 978 G=0.995 A=0.005
1000Genomes American Sub 694 G=0.988 A=0.012
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9763 A=0.0237
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9842 A=0.0158
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9857 A=0.0143
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.979 A=0.021
Northern Sweden ACPOP Study-wide 600 G=0.978 A=0.022
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.970 A=0.030
FINRISK Finnish from FINRISK project Study-wide 304 G=0.990 A=0.010
Qatari Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 8 G=0.5 A=0.5
Siberian Global Study-wide 6 G=0.5 A=0.5
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.p13 chr 8 NC_000008.11:g.27463672= NC_000008.11:g.27463672G>A
GRCh37.p13 chr 8 NC_000008.10:g.27321189= NC_000008.10:g.27321189G>A
CHRNA2 RefSeqGene NG_015827.1:g.20625= NG_015827.1:g.20625C>T
CHRNA2 transcript variant 1 NM_000742.4:c.771= NM_000742.4:c.771C>T
CHRNA2 transcript variant 1 NM_000742.3:c.771= NM_000742.3:c.771C>T
CHRNA2 transcript variant 4 NM_001347706.2:c.294= NM_001347706.2:c.294C>T
CHRNA2 transcript variant 4 NM_001347706.1:c.294= NM_001347706.1:c.294C>T
CHRNA2 transcript variant 2 NM_001282455.2:c.726= NM_001282455.2:c.726C>T
CHRNA2 transcript variant 2 NM_001282455.1:c.726= NM_001282455.1:c.726C>T
CHRNA2 transcript variant 3 NM_001347705.2:c.294= NM_001347705.2:c.294C>T
CHRNA2 transcript variant 3 NM_001347705.1:c.294= NM_001347705.1:c.294C>T
CHRNA2 transcript variant 5 NM_001347707.2:c.177= NM_001347707.2:c.177C>T
CHRNA2 transcript variant 5 NM_001347707.1:c.177= NM_001347707.1:c.177C>T
CHRNA2 transcript variant 6 NM_001347708.2:c.177= NM_001347708.2:c.177C>T
CHRNA2 transcript variant 6 NM_001347708.1:c.177= NM_001347708.1:c.177C>T
CHRNA2 transcript variant X1 XM_011544389.2:c.177= XM_011544389.2:c.177C>T
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Tyr257= NP_000733.2:p.Tyr257=
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Tyr98= NP_001334635.1:p.Tyr98=
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Tyr242= NP_001269384.1:p.Tyr242=
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Tyr98= NP_001334634.1:p.Tyr98=
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Tyr59= NP_001334636.1:p.Tyr59=
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Tyr59= NP_001334637.1:p.Tyr59=
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Tyr59= XP_011542691.1:p.Tyr59=
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#.

54 SubSNP, 17 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 UUGC ss76901686 Dec 07, 2007 (129)
2 PERLEGEN ss161151683 Dec 01, 2009 (131)
3 1000GENOMES ss210708330 Jul 14, 2010 (132)
4 1000GENOMES ss334772661 May 09, 2011 (134)
5 NHLBI-ESP ss342255734 May 09, 2011 (134)
6 1000GENOMES ss490962667 May 04, 2012 (137)
7 EXOME_CHIP ss491411863 May 04, 2012 (137)
8 CLINSEQ_SNP ss491923165 May 04, 2012 (137)
9 ILLUMINA ss783476861 Sep 08, 2015 (146)
10 EVA-GONL ss985336399 Aug 21, 2014 (142)
11 1000GENOMES ss1329152888 Aug 21, 2014 (142)
12 DDI ss1431461521 Apr 01, 2015 (144)
13 CLINVAR ss1457613778 Nov 23, 2014 (142)
14 EVA_FINRISK ss1584057810 Apr 01, 2015 (144)
15 EVA_DECODE ss1594929044 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1620263928 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1663257961 Apr 01, 2015 (144)
18 EVA_EXAC ss1689143428 Apr 01, 2015 (144)
19 EVA_MGP ss1711197085 Apr 01, 2015 (144)
20 ILLUMINA ss1752727077 Sep 08, 2015 (146)
21 ILLUMINA ss1917827147 Feb 12, 2016 (147)
22 WEILL_CORNELL_DGM ss1928625185 Feb 12, 2016 (147)
23 ILLUMINA ss1946233313 Feb 12, 2016 (147)
24 ILLUMINA ss1959099756 Feb 12, 2016 (147)
25 ILLUMINA ss2094987047 Dec 20, 2016 (150)
26 USC_VALOUEV ss2153236950 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2301783588 Dec 20, 2016 (150)
28 TOPMED ss2471440444 Dec 20, 2016 (150)
29 GNOMAD ss2737071313 Nov 08, 2017 (151)
30 GNOMAD ss2748023062 Nov 08, 2017 (151)
31 GNOMAD ss2864754037 Nov 08, 2017 (151)
32 AFFY ss2985435065 Nov 08, 2017 (151)
33 AFFY ss2986079021 Nov 08, 2017 (151)
34 SWEGEN ss3002899140 Nov 08, 2017 (151)
35 ILLUMINA ss3022832459 Nov 08, 2017 (151)
36 CSHL ss3348109199 Nov 08, 2017 (151)
37 TOPMED ss3557398141 Nov 08, 2017 (151)
38 ILLUMINA ss3635165532 Oct 12, 2018 (152)
39 ILLUMINA ss3640872822 Oct 12, 2018 (152)
40 ILLUMINA ss3653373732 Oct 12, 2018 (152)
41 ILLUMINA ss3654197024 Oct 12, 2018 (152)
42 EGCUT_WGS ss3670583357 Jul 13, 2019 (153)
43 EVA_DECODE ss3721677202 Jul 13, 2019 (153)
44 ACPOP ss3735520102 Jul 13, 2019 (153)
45 ILLUMINA ss3744578640 Jul 13, 2019 (153)
46 ILLUMINA ss3745465333 Jul 13, 2019 (153)
47 EVA ss3767793414 Jul 13, 2019 (153)
48 ILLUMINA ss3772957866 Jul 13, 2019 (153)
49 EVA ss3824358558 Apr 26, 2020 (154)
50 EVA ss3825738743 Apr 26, 2020 (154)
51 SGDP_PRJ ss3869562656 Apr 26, 2020 (154)
52 FSA-LAB ss3984396112 Apr 26, 2021 (155)
53 EVA ss3986418607 Apr 26, 2021 (155)
54 TOPMED ss4780089182 Apr 26, 2021 (155)
55 1000Genomes NC_000008.10 - 27321189 Oct 12, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 27321189 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000008.10 - 27321189 Oct 12, 2018 (152)
58 ExAC NC_000008.10 - 27321189 Oct 12, 2018 (152)
59 FINRISK NC_000008.10 - 27321189 Apr 26, 2020 (154)
60 gnomAD - Genomes NC_000008.11 - 27463672 Apr 26, 2021 (155)
61 gnomAD - Exomes NC_000008.10 - 27321189 Jul 13, 2019 (153)
62 GO Exome Sequencing Project NC_000008.10 - 27321189 Oct 12, 2018 (152)
63 Genome of the Netherlands Release 5 NC_000008.10 - 27321189 Apr 26, 2020 (154)
64 Medical Genome Project healthy controls from Spanish population NC_000008.10 - 27321189 Apr 26, 2020 (154)
65 Northern Sweden NC_000008.10 - 27321189 Jul 13, 2019 (153)
66 Qatari NC_000008.10 - 27321189 Apr 26, 2020 (154)
67 SGDP_PRJ NC_000008.10 - 27321189 Apr 26, 2020 (154)
68 Siberian NC_000008.10 - 27321189 Apr 26, 2020 (154)
69 TopMed NC_000008.11 - 27463672 Apr 26, 2021 (155)
70 UK 10K study - Twins NC_000008.10 - 27321189 Oct 12, 2018 (152)
71 ALFA NC_000008.11 - 27463672 Apr 26, 2021 (155)
72 ClinVar RCV000116714.2 Oct 12, 2018 (152)
73 ClinVar RCV000369041.2 Apr 26, 2021 (155)
74 ClinVar RCV000460445.3 Apr 26, 2021 (155)
75 ClinVar RCV000716400.1 Jul 13, 2019 (153)
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
ss210708330, ss491923165, ss1594929044, ss2094987047 NC_000008.9:27377105:G:A NC_000008.11:27463671:G:A (self)
41255182, 22938968, 16321605, 9239251, 54271, 6241272, 816404, 10249077, 312845, 8804967, 10667115, 21579636, 5753304, 22938968, ss334772661, ss342255734, ss490962667, ss491411863, ss783476861, ss985336399, ss1329152888, ss1431461521, ss1584057810, ss1620263928, ss1663257961, ss1689143428, ss1711197085, ss1752727077, ss1917827147, ss1928625185, ss1946233313, ss1959099756, ss2153236950, ss2471440444, ss2737071313, ss2748023062, ss2864754037, ss2985435065, ss2986079021, ss3002899140, ss3022832459, ss3348109199, ss3635165532, ss3640872822, ss3653373732, ss3654197024, ss3670583357, ss3735520102, ss3744578640, ss3745465333, ss3767793414, ss3772957866, ss3824358558, ss3825738743, ss3869562656, ss3984396112, ss3986418607 NC_000008.10:27321188:G:A NC_000008.11:27463671:G:A (self)
RCV000116714.2, RCV000369041.2, RCV000460445.3, RCV000716400.1, 290884983, 385907301, 617466742, 10463216628, ss1457613778, ss2301783588, ss3557398141, ss3721677202, ss4780089182 NC_000008.11:27463671:G:A NC_000008.11:27463671:G:A (self)
ss76901686, ss161151683 NT_167187.1:15179334:G:A NC_000008.11:27463671:G:A (self)
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Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs56229264

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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