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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.

rs56298562

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:27463119 (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=0.015225 (4030/264690, TOPMED)
A=0.022361 (5608/250796, GnomAD_exome)
A=0.017598 (2469/140300, GnomAD) (+ 17 more)
A=0.023088 (2770/119974, ExAC)
A=0.02292 (1130/49310, ALFA)
A=0.00042 (7/16760, 8.3KJPN)
A=0.01768 (230/13006, GO-ESP)
A=0.0134 (67/5008, 1000G)
A=0.0161 (72/4480, Estonian)
A=0.0262 (101/3854, ALSPAC)
A=0.0272 (101/3708, TWINSUK)
A=0.0024 (7/2922, KOREAN)
A=0.0033 (6/1832, Korea1K)
A=0.031 (31/998, GoNL)
A=0.020 (12/600, NorthernSweden)
A=0.004 (2/534, MGP)
A=0.030 (9/304, FINRISK)
A=0.019 (4/216, Qatari)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
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.27463119G>A
GRCh37.p13 chr 8 NC_000008.10:g.27320636G>A
CHRNA2 RefSeqGene NG_015827.1:g.21178C>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.1324C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Leu442= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant 3 NM_001347705.2:c.847C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Leu283= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant 6 NM_001347708.2:c.730C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Leu244= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant 5 NM_001347707.2:c.730C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Leu244= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant 4 NM_001347706.2:c.847C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Leu283= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.1279C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Leu427= L (Leu) > L (Leu) Synonymous Variant
CHRNA2 transcript variant X1 XM_011544389.2:c.730C>T L [CTG] > L [TTG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Leu244= L (Leu) > L (Leu) 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: 134186 )
ClinVar Accession Disease Names Clinical Significance
RCV000116710.5 not specified Benign
RCV000230291.4 Autosomal dominant nocturnal frontal lobe epilepsy Benign
RCV000347213.2 Epilepsy, nocturnal frontal lobe, type 4 Benign
RCV000715706.1 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 49310 G=0.97708 A=0.02292
European Sub 37284 G=0.97465 A=0.02535
African Sub 3574 G=0.9938 A=0.0062
African Others Sub 122 G=1.000 A=0.000
African American Sub 3452 G=0.9936 A=0.0064
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=0.990 A=0.010
Latin American 2 Sub 628 G=0.989 A=0.011
South Asian Sub 98 G=0.95 A=0.05
Other Sub 7058 G=0.9793 A=0.0207


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=0.984775 A=0.015225
gnomAD - Exomes Global Study-wide 250796 G=0.977639 A=0.022361
gnomAD - Exomes European Sub 134922 G=0.972807 A=0.027193
gnomAD - Exomes Asian Sub 48942 G=0.97509 A=0.02491
gnomAD - Exomes American Sub 34546 G=0.99106 A=0.00894
gnomAD - Exomes African Sub 16248 G=0.99643 A=0.00357
gnomAD - Exomes Ashkenazi Jewish Sub 10028 G=0.97716 A=0.02284
gnomAD - Exomes Other Sub 6110 G=0.9797 A=0.0203
gnomAD - Genomes Global Study-wide 140300 G=0.982402 A=0.017598
gnomAD - Genomes European Sub 75956 G=0.97385 A=0.02615
gnomAD - Genomes African Sub 42068 G=0.99624 A=0.00376
gnomAD - Genomes American Sub 13664 G=0.98514 A=0.01486
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9738 A=0.0262
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9838 A=0.0162
ExAC Global Study-wide 119974 G=0.976912 A=0.023088
ExAC Europe Sub 72870 G=0.97312 A=0.02688
ExAC Asian Sub 24282 G=0.97278 A=0.02722
ExAC American Sub 11554 G=0.99273 A=0.00727
ExAC African Sub 10380 G=0.99615 A=0.00385
ExAC Other Sub 888 G=0.971 A=0.029
8.3KJPN JAPANESE Study-wide 16760 G=0.99958 A=0.00042
GO Exome Sequencing Project Global Study-wide 13006 G=0.98232 A=0.01768
GO Exome Sequencing Project European American Sub 8600 G=0.9757 A=0.0243
GO Exome Sequencing Project African American Sub 4406 G=0.9952 A=0.0048
1000Genomes Global Study-wide 5008 G=0.9866 A=0.0134
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=0.9761 A=0.0239
1000Genomes South Asian Sub 978 G=0.965 A=0.035
1000Genomes American Sub 694 G=0.988 A=0.012
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9839 A=0.0161
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9738 A=0.0262
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9728 A=0.0272
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9976 A=0.0024
Korean Genome Project KOREAN Study-wide 1832 G=0.9967 A=0.0033
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.969 A=0.031
Northern Sweden ACPOP Study-wide 600 G=0.980 A=0.020
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.996 A=0.004
FINRISK Finnish from FINRISK project Study-wide 304 G=0.970 A=0.030
Qatari Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 8 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.27463119= NC_000008.11:g.27463119G>A
GRCh37.p13 chr 8 NC_000008.10:g.27320636= NC_000008.10:g.27320636G>A
CHRNA2 RefSeqGene NG_015827.1:g.21178= NG_015827.1:g.21178C>T
CHRNA2 transcript variant 1 NM_000742.4:c.1324= NM_000742.4:c.1324C>T
CHRNA2 transcript variant 1 NM_000742.3:c.1324= NM_000742.3:c.1324C>T
CHRNA2 transcript variant 4 NM_001347706.2:c.847= NM_001347706.2:c.847C>T
CHRNA2 transcript variant 4 NM_001347706.1:c.847= NM_001347706.1:c.847C>T
CHRNA2 transcript variant 2 NM_001282455.2:c.1279= NM_001282455.2:c.1279C>T
CHRNA2 transcript variant 2 NM_001282455.1:c.1279= NM_001282455.1:c.1279C>T
CHRNA2 transcript variant 3 NM_001347705.2:c.847= NM_001347705.2:c.847C>T
CHRNA2 transcript variant 3 NM_001347705.1:c.847= NM_001347705.1:c.847C>T
CHRNA2 transcript variant 5 NM_001347707.2:c.730= NM_001347707.2:c.730C>T
CHRNA2 transcript variant 5 NM_001347707.1:c.730= NM_001347707.1:c.730C>T
CHRNA2 transcript variant 6 NM_001347708.2:c.730= NM_001347708.2:c.730C>T
CHRNA2 transcript variant 6 NM_001347708.1:c.730= NM_001347708.1:c.730C>T
CHRNA2 transcript variant X1 XM_011544389.2:c.730= XM_011544389.2:c.730C>T
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Leu442= NP_000733.2:p.Leu442=
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Leu283= NP_001334635.1:p.Leu283=
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Leu427= NP_001269384.1:p.Leu427=
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Leu283= NP_001334634.1:p.Leu283=
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Leu244= NP_001334636.1:p.Leu244=
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Leu244= NP_001334637.1:p.Leu244=
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Leu244= XP_011542691.1:p.Leu244=
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#.

44 SubSNP, 19 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 UUGC ss76901821 Dec 07, 2007 (129)
2 PERLEGEN ss161151689 Dec 01, 2009 (131)
3 1000GENOMES ss334772660 May 09, 2011 (134)
4 NHLBI-ESP ss342255718 May 09, 2011 (134)
5 1000GENOMES ss490962663 May 04, 2012 (137)
6 CLINSEQ_SNP ss491923164 May 04, 2012 (137)
7 SSMP ss655076040 Apr 25, 2013 (138)
8 EVA-GONL ss985336398 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1067496632 Aug 21, 2014 (142)
10 1000GENOMES ss1329152876 Aug 21, 2014 (142)
11 CLINVAR ss1457613774 Nov 23, 2014 (142)
12 EVA_FINRISK ss1584057807 Apr 01, 2015 (144)
13 EVA_DECODE ss1594929040 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1620263923 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1663257956 Apr 01, 2015 (144)
16 EVA_EXAC ss1689143302 Apr 01, 2015 (144)
17 EVA_MGP ss1711197084 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1928625180 Feb 12, 2016 (147)
19 JJLAB ss2025015245 Sep 14, 2016 (149)
20 HUMAN_LONGEVITY ss2301783549 Dec 20, 2016 (150)
21 TOPMED ss2471440414 Dec 20, 2016 (150)
22 GNOMAD ss2737071140 Nov 08, 2017 (151)
23 GNOMAD ss2748023006 Nov 08, 2017 (151)
24 GNOMAD ss2864753981 Nov 08, 2017 (151)
25 SWEGEN ss3002899131 Nov 08, 2017 (151)
26 CSHL ss3348109198 Nov 08, 2017 (151)
27 TOPMED ss3557398033 Nov 08, 2017 (151)
28 OMUKHERJEE_ADBS ss3646373926 Oct 12, 2018 (152)
29 EGCUT_WGS ss3670583351 Jul 13, 2019 (153)
30 EVA_DECODE ss3721677196 Jul 13, 2019 (153)
31 ACPOP ss3735520099 Jul 13, 2019 (153)
32 EVA ss3767793408 Jul 13, 2019 (153)
33 EVA ss3824358531 Apr 26, 2020 (154)
34 EVA ss3825738742 Apr 26, 2020 (154)
35 EVA ss3839052514 Apr 26, 2020 (154)
36 EVA ss3844510797 Apr 26, 2020 (154)
37 SGDP_PRJ ss3869562649 Apr 26, 2020 (154)
38 KRGDB ss3916998016 Apr 26, 2020 (154)
39 KOGIC ss3963523186 Apr 26, 2020 (154)
40 FSA-LAB ss3984396110 Apr 26, 2021 (155)
41 EVA ss3986418603 Apr 26, 2021 (155)
42 TOPMED ss4780089010 Apr 26, 2021 (155)
43 TOMMO_GENOMICS ss5187917143 Apr 26, 2021 (155)
44 EVA ss5237041720 Apr 26, 2021 (155)
45 1000Genomes NC_000008.10 - 27320636 Oct 12, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 27320636 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000008.10 - 27320636 Oct 12, 2018 (152)
48 ExAC NC_000008.10 - 27320636 Oct 12, 2018 (152)
49 FINRISK NC_000008.10 - 27320636 Apr 26, 2020 (154)
50 gnomAD - Genomes NC_000008.11 - 27463119 Apr 26, 2021 (155)
51 gnomAD - Exomes NC_000008.10 - 27320636 Jul 13, 2019 (153)
52 GO Exome Sequencing Project NC_000008.10 - 27320636 Oct 12, 2018 (152)
53 Genome of the Netherlands Release 5 NC_000008.10 - 27320636 Apr 26, 2020 (154)
54 KOREAN population from KRGDB NC_000008.10 - 27320636 Apr 26, 2020 (154)
55 Korean Genome Project NC_000008.11 - 27463119 Apr 26, 2020 (154)
56 Medical Genome Project healthy controls from Spanish population NC_000008.10 - 27320636 Apr 26, 2020 (154)
57 Northern Sweden NC_000008.10 - 27320636 Jul 13, 2019 (153)
58 Qatari NC_000008.10 - 27320636 Apr 26, 2020 (154)
59 SGDP_PRJ NC_000008.10 - 27320636 Apr 26, 2020 (154)
60 8.3KJPN NC_000008.10 - 27320636 Apr 26, 2021 (155)
61 TopMed NC_000008.11 - 27463119 Apr 26, 2021 (155)
62 UK 10K study - Twins NC_000008.10 - 27320636 Oct 12, 2018 (152)
63 ALFA NC_000008.11 - 27463119 Apr 26, 2021 (155)
64 ClinVar RCV000116710.5 Oct 12, 2018 (152)
65 ClinVar RCV000230291.4 Apr 26, 2021 (155)
66 ClinVar RCV000347213.2 Apr 26, 2021 (155)
67 ClinVar RCV000715706.1 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
ss491923164, ss1594929040 NC_000008.9:27376552:G:A NC_000008.11:27463118:G:A (self)
41255170, 22938963, 16321599, 9239121, 54268, 6241075, 816377, 10249076, 24175410, 312844, 8804964, 10667110, 21579629, 45886450, 22938963, ss334772660, ss342255718, ss490962663, ss655076040, ss985336398, ss1067496632, ss1329152876, ss1584057807, ss1620263923, ss1663257956, ss1689143302, ss1711197084, ss1928625180, ss2025015245, ss2471440414, ss2737071140, ss2748023006, ss2864753981, ss3002899131, ss3348109198, ss3646373926, ss3670583351, ss3735520099, ss3767793408, ss3824358531, ss3825738742, ss3839052514, ss3869562649, ss3916998016, ss3984396110, ss3986418603, ss5187917143 NC_000008.10:27320635:G:A NC_000008.11:27463118:G:A (self)
RCV000116710.5, RCV000230291.4, RCV000347213.2, RCV000715706.1, 290884857, 19901187, 385907202, 617466570, 10080560787, ss1457613774, ss2301783549, ss3557398033, ss3721677196, ss3844510797, ss3963523186, ss4780089010, ss5237041720 NC_000008.11:27463118:G:A NC_000008.11:27463118:G:A (self)
ss76901821, ss161151689 NT_167187.1:15178781:G:A NC_000008.11:27463118:G:A (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 rs56298562

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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
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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