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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.

rs74772771

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:27469915 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000329 (87/264690, TOPMED)
A=0.000595 (118/198440, ALFA)
A=0.000364 (51/140284, GnomAD) (+ 7 more)
A=0.00014 (11/78698, PAGE_STUDY)
A=0.00023 (3/13006, GO-ESP)
A=0.0004 (2/5008, 1000G)
A=0.0008 (3/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.001 (1/998, GoNL)
A=0.002 (1/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNA2 : Missense 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.27469915G>A
GRCh38.p13 chr 8 NC_000008.11:g.27469915G>C
GRCh37.p13 chr 8 NC_000008.10:g.27327432G>A
GRCh37.p13 chr 8 NC_000008.10:g.27327432G>C
CHRNA2 RefSeqGene NG_015827.1:g.14382C>T
CHRNA2 RefSeqGene NG_015827.1:g.14382C>G
Gene: CHRNA2, cholinergic receptor nicotinic alpha 2 subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNA2 transcript variant 3 NM_001347705.2:c.-288= N/A 5 Prime UTR Variant
CHRNA2 transcript variant 6 NM_001347708.2:c.-322= N/A 5 Prime UTR Variant
CHRNA2 transcript variant 5 NM_001347707.2:c.-274= N/A 5 Prime UTR Variant
CHRNA2 transcript variant 4 NM_001347706.2:c.-333= N/A 5 Prime UTR Variant
CHRNA2 transcript variant 1 NM_000742.4:c.140C>T T [ACG] > M [ATG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Thr47Met T (Thr) > M (Met) Missense Variant
CHRNA2 transcript variant 1 NM_000742.4:c.140C>G T [ACG] > R [AGG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Thr47Arg T (Thr) > R (Arg) Missense Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.140C>T T [ACG] > M [ATG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Thr47Met T (Thr) > M (Met) Missense Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.140C>G T [ACG] > R [AGG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Thr47Arg T (Thr) > R (Arg) Missense Variant
CHRNA2 transcript variant X1 XM_011544389.2:c.-319= N/A 5 Prime UTR 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: 202268 )
ClinVar Accession Disease Names Clinical Significance
RCV000615228.3 Epilepsy, nocturnal frontal lobe, type 4 Conflicting-Interpretations-Of-Pathogenicity
RCV000727343.6 not provided Uncertain-Significance
RCV001079768.1 Autosomal dominant nocturnal frontal lobe epilepsy Likely-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 198440 G=0.999405 A=0.000595
European Sub 169724 G=0.999346 A=0.000654
African Sub 4520 G=1.0000 A=0.0000
African Others Sub 176 G=1.000 A=0.000
African American Sub 4344 G=1.0000 A=0.0000
Asian Sub 6312 G=1.0000 A=0.0000
East Asian Sub 4466 G=1.0000 A=0.0000
Other Asian Sub 1846 G=1.0000 A=0.0000
Latin American 1 Sub 790 G=1.000 A=0.000
Latin American 2 Sub 966 G=1.000 A=0.000
South Asian Sub 274 G=1.000 A=0.000
Other Sub 15854 G=0.99956 A=0.00044


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=0.999671 A=0.000329
gnomAD - Genomes Global Study-wide 140284 G=0.999636 A=0.000364
gnomAD - Genomes European Sub 75956 G=0.99943 A=0.00057
gnomAD - Genomes African Sub 42056 G=0.99988 A=0.00012
gnomAD - Genomes American Sub 13662 G=0.99985 A=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9995 A=0.0005
The PAGE Study Global Study-wide 78698 G=0.99986 A=0.00014
The PAGE Study AfricanAmerican Sub 32514 G=0.99985 A=0.00015
The PAGE Study Mexican Sub 10810 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8316 G=0.9999 A=0.0001
The PAGE Study PuertoRican Sub 7918 G=0.9999 A=0.0001
The PAGE Study NativeHawaiian Sub 4534 G=0.9996 A=0.0004
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99977 A=0.00023
GO Exome Sequencing Project European American Sub 8600 G=0.9997 A=0.0003
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9992 A=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9995 A=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.999 A=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
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 C
GRCh38.p13 chr 8 NC_000008.11:g.27469915= NC_000008.11:g.27469915G>A NC_000008.11:g.27469915G>C
GRCh37.p13 chr 8 NC_000008.10:g.27327432= NC_000008.10:g.27327432G>A NC_000008.10:g.27327432G>C
CHRNA2 RefSeqGene NG_015827.1:g.14382= NG_015827.1:g.14382C>T NG_015827.1:g.14382C>G
CHRNA2 transcript variant 1 NM_000742.4:c.140= NM_000742.4:c.140C>T NM_000742.4:c.140C>G
CHRNA2 transcript variant 1 NM_000742.3:c.140= NM_000742.3:c.140C>T NM_000742.3:c.140C>G
CHRNA2 transcript variant 4 NM_001347706.2:c.-333= NM_001347706.2:c.-333C>T NM_001347706.2:c.-333C>G
CHRNA2 transcript variant 4 NM_001347706.1:c.-333= NM_001347706.1:c.-333C>T NM_001347706.1:c.-333C>G
CHRNA2 transcript variant 2 NM_001282455.2:c.140= NM_001282455.2:c.140C>T NM_001282455.2:c.140C>G
CHRNA2 transcript variant 2 NM_001282455.1:c.140= NM_001282455.1:c.140C>T NM_001282455.1:c.140C>G
CHRNA2 transcript variant 3 NM_001347705.2:c.-288= NM_001347705.2:c.-288C>T NM_001347705.2:c.-288C>G
CHRNA2 transcript variant 3 NM_001347705.1:c.-288= NM_001347705.1:c.-288C>T NM_001347705.1:c.-288C>G
CHRNA2 transcript variant 5 NM_001347707.2:c.-274= NM_001347707.2:c.-274C>T NM_001347707.2:c.-274C>G
CHRNA2 transcript variant 5 NM_001347707.1:c.-274= NM_001347707.1:c.-274C>T NM_001347707.1:c.-274C>G
CHRNA2 transcript variant 6 NM_001347708.2:c.-322= NM_001347708.2:c.-322C>T NM_001347708.2:c.-322C>G
CHRNA2 transcript variant 6 NM_001347708.1:c.-322= NM_001347708.1:c.-322C>T NM_001347708.1:c.-322C>G
CHRNA2 transcript variant X1 XM_011544389.2:c.-319= XM_011544389.2:c.-319C>T XM_011544389.2:c.-319C>G
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Thr47= NP_000733.2:p.Thr47Met NP_000733.2:p.Thr47Arg
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Thr47= NP_001269384.1:p.Thr47Met NP_001269384.1:p.Thr47Arg
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#.

40 SubSNP, 14 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss161151701 Dec 01, 2009 (131)
2 1000GENOMES ss488885922 May 04, 2012 (137)
3 EXOME_CHIP ss491411870 May 04, 2012 (137)
4 CLINSEQ_SNP ss491923172 May 04, 2012 (137)
5 NHLBI-ESP ss712834855 Apr 25, 2013 (138)
6 ILLUMINA ss780868673 Sep 08, 2015 (146)
7 ILLUMINA ss783553672 Sep 08, 2015 (146)
8 EVA-GONL ss985336453 Aug 21, 2014 (142)
9 1000GENOMES ss1329153094 Aug 21, 2014 (142)
10 EVA_DECODE ss1594929110 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1620264052 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1663258085 Apr 01, 2015 (144)
13 EVA_EXAC ss1689143630 Apr 01, 2015 (144)
14 EVA_EXAC ss1689143631 Apr 01, 2015 (144)
15 EVA_MGP ss1711197094 Apr 01, 2015 (144)
16 ILLUMINA ss1752727086 Sep 08, 2015 (146)
17 ILLUMINA ss1917827152 Feb 12, 2016 (147)
18 ILLUMINA ss1946233320 Feb 12, 2016 (147)
19 ILLUMINA ss1959099771 Feb 12, 2016 (147)
20 HUMAN_LONGEVITY ss2301783998 Dec 20, 2016 (150)
21 TOPMED ss2471440868 Dec 20, 2016 (150)
22 GNOMAD ss2737071601 Nov 08, 2017 (151)
23 GNOMAD ss2748023160 Nov 08, 2017 (151)
24 GNOMAD ss2864754560 Nov 08, 2017 (151)
25 AFFY ss2985435074 Nov 08, 2017 (151)
26 AFFY ss2986079056 Nov 08, 2017 (151)
27 SWEGEN ss3002899215 Nov 08, 2017 (151)
28 TOPMED ss3557399307 Nov 08, 2017 (151)
29 ILLUMINA ss3630028361 Oct 12, 2018 (152)
30 ILLUMINA ss3635165541 Oct 12, 2018 (152)
31 ILLUMINA ss3640872831 Oct 12, 2018 (152)
32 ILLUMINA ss3644966506 Oct 12, 2018 (152)
33 ILLUMINA ss3654197033 Oct 12, 2018 (152)
34 EVA_DECODE ss3721677284 Jul 13, 2019 (153)
35 ILLUMINA ss3744578645 Jul 13, 2019 (153)
36 ILLUMINA ss3745465342 Jul 13, 2019 (153)
37 PAGE_CC ss3771433264 Jul 13, 2019 (153)
38 ILLUMINA ss3772957875 Jul 13, 2019 (153)
39 EVA ss3824358601 Apr 26, 2020 (154)
40 TOPMED ss4780090788 Apr 26, 2021 (155)
41 1000Genomes NC_000008.10 - 27327432 Oct 12, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 27327432 Oct 12, 2018 (152)
43 ExAC

Submission ignored due to conflicting rows:
Row 9239463 (NC_000008.10:27327431:G:G 120824/120884, NC_000008.10:27327431:G:A 60/120884)
Row 9239464 (NC_000008.10:27327431:G:G 120883/120884, NC_000008.10:27327431:G:C 1/120884)

- Oct 12, 2018 (152)
44 ExAC

Submission ignored due to conflicting rows:
Row 9239463 (NC_000008.10:27327431:G:G 120824/120884, NC_000008.10:27327431:G:A 60/120884)
Row 9239464 (NC_000008.10:27327431:G:G 120883/120884, NC_000008.10:27327431:G:C 1/120884)

- Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000008.11 - 27469915 Apr 26, 2021 (155)
46 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6241568 (NC_000008.10:27327431:G:G 251128/251244, NC_000008.10:27327431:G:A 116/251244)
Row 6241569 (NC_000008.10:27327431:G:G 251243/251244, NC_000008.10:27327431:G:C 1/251244)

- Jul 13, 2019 (153)
47 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6241568 (NC_000008.10:27327431:G:G 251128/251244, NC_000008.10:27327431:G:A 116/251244)
Row 6241569 (NC_000008.10:27327431:G:G 251243/251244, NC_000008.10:27327431:G:C 1/251244)

- Jul 13, 2019 (153)
48 GO Exome Sequencing Project NC_000008.10 - 27327432 Oct 12, 2018 (152)
49 Genome of the Netherlands Release 5 NC_000008.10 - 27327432 Apr 26, 2020 (154)
50 Medical Genome Project healthy controls from Spanish population NC_000008.10 - 27327432 Apr 26, 2020 (154)
51 The PAGE Study NC_000008.11 - 27469915 Jul 13, 2019 (153)
52 TopMed NC_000008.11 - 27469915 Apr 26, 2021 (155)
53 UK 10K study - Twins NC_000008.10 - 27327432 Oct 12, 2018 (152)
54 ALFA NC_000008.11 - 27469915 Apr 26, 2021 (155)
55 ClinVar RCV000615228.3 Apr 26, 2021 (155)
56 ClinVar RCV000727343.6 Apr 26, 2021 (155)
57 ClinVar RCV001079768.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491923172, ss1594929110 NC_000008.9:27383348:G:A NC_000008.11:27469914:G:A (self)
41255395, 22939096, 816447, 10249131, 312854, 22939096, ss488885922, ss491411870, ss712834855, ss780868673, ss783553672, ss985336453, ss1329153094, ss1620264052, ss1663258085, ss1689143630, ss1711197094, ss1752727086, ss1917827152, ss1946233320, ss1959099771, ss2471440868, ss2737071601, ss2748023160, ss2864754560, ss2985435074, ss2986079056, ss3002899215, ss3630028361, ss3635165541, ss3640872831, ss3644966506, ss3654197033, ss3744578645, ss3745465342, ss3772957875, ss3824358601 NC_000008.10:27327431:G:A NC_000008.11:27469914:G:A (self)
RCV000615228.3, RCV000727343.6, RCV001079768.1, 290886248, 654733, 385908300, 617468348, 5489511616, ss2301783998, ss3557399307, ss3721677284, ss3771433264, ss4780090788 NC_000008.11:27469914:G:A NC_000008.11:27469914:G:A (self)
ss161151701 NT_167187.1:15185577:G:A NC_000008.11:27469914:G:A (self)
ss1689143631, ss2737071601 NC_000008.10:27327431:G:C NC_000008.11:27469914:G:C (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 rs74772771

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