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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.

rs77769511

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:27463666 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000032 (8/251440, GnomAD_exome)
A=0.000043 (6/140228, GnomAD)
A=0.000025 (3/121392, ExAC) (+ 3 more)
A=0.00009 (2/23038, ALFA)
A=0.00006 (1/16760, 8.3KJPN)
A=0.00008 (1/13006, GO-ESP)
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.27463666G>A
GRCh38.p13 chr 8 NC_000008.11:g.27463666G>T
GRCh37.p13 chr 8 NC_000008.10:g.27321183G>A
GRCh37.p13 chr 8 NC_000008.10:g.27321183G>T
CHRNA2 RefSeqGene NG_015827.1:g.20631C>T
CHRNA2 RefSeqGene NG_015827.1:g.20631C>A
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.777C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Phe259= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 1 NM_000742.4:c.777C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Phe259Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant 3 NM_001347705.2:c.300C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Phe100= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 3 NM_001347705.2:c.300C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Phe100Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant 6 NM_001347708.2:c.183C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Phe61= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 6 NM_001347708.2:c.183C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Phe61Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant 5 NM_001347707.2:c.183C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Phe61= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 5 NM_001347707.2:c.183C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Phe61Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant 4 NM_001347706.2:c.300C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Phe100= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 4 NM_001347706.2:c.300C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Phe100Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.732C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Phe244= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant 2 NM_001282455.2:c.732C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Phe244Leu F (Phe) > L (Leu) Missense Variant
CHRNA2 transcript variant X1 XM_011544389.2:c.183C>T F [TTC] > F [TTT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Phe61= F (Phe) > F (Phe) Synonymous Variant
CHRNA2 transcript variant X1 XM_011544389.2:c.183C>A F [TTC] > L [TTA] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Phe61Leu F (Phe) > L (Leu) Missense 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: 502692 )
ClinVar Accession Disease Names Clinical Significance
RCV000608557.1 not specified 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 23038 G=0.99991 A=0.00009, T=0.00000
European Sub 15752 G=0.99994 A=0.00006, T=0.00000
African Sub 3492 G=1.0000 A=0.0000, T=0.0000
African Others Sub 122 G=1.000 A=0.000, T=0.000
African American Sub 3370 G=1.0000 A=0.0000, T=0.0000
Asian Sub 168 G=0.994 A=0.006, T=0.000
East Asian Sub 112 G=0.991 A=0.009, T=0.000
Other Asian Sub 56 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, T=0.00
Other Sub 2772 G=1.0000 A=0.0000, T=0.0000


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
gnomAD - Exomes Global Study-wide 251440 G=0.999968 A=0.000032
gnomAD - Exomes European Sub 135372 G=0.999978 A=0.000022
gnomAD - Exomes Asian Sub 49010 G=0.99992 A=0.00008
gnomAD - Exomes American Sub 34592 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16254 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6136 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140228 G=0.999957 A=0.000043
gnomAD - Genomes European Sub 75938 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42028 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13656 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 121392 G=0.999975 A=0.000025
ExAC Europe Sub 73338 G=0.99999 A=0.00001
ExAC Asian Sub 25166 G=0.99992 A=0.00008
ExAC American Sub 11578 G=1.00000 A=0.00000
ExAC African Sub 10404 G=1.00000 A=0.00000
ExAC Other Sub 906 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
GO Exome Sequencing Project Global Study-wide 13006 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
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 T
GRCh38.p13 chr 8 NC_000008.11:g.27463666= NC_000008.11:g.27463666G>A NC_000008.11:g.27463666G>T
GRCh37.p13 chr 8 NC_000008.10:g.27321183= NC_000008.10:g.27321183G>A NC_000008.10:g.27321183G>T
CHRNA2 RefSeqGene NG_015827.1:g.20631= NG_015827.1:g.20631C>T NG_015827.1:g.20631C>A
CHRNA2 transcript variant 1 NM_000742.4:c.777= NM_000742.4:c.777C>T NM_000742.4:c.777C>A
CHRNA2 transcript variant 1 NM_000742.3:c.777= NM_000742.3:c.777C>T NM_000742.3:c.777C>A
CHRNA2 transcript variant 4 NM_001347706.2:c.300= NM_001347706.2:c.300C>T NM_001347706.2:c.300C>A
CHRNA2 transcript variant 4 NM_001347706.1:c.300= NM_001347706.1:c.300C>T NM_001347706.1:c.300C>A
CHRNA2 transcript variant 2 NM_001282455.2:c.732= NM_001282455.2:c.732C>T NM_001282455.2:c.732C>A
CHRNA2 transcript variant 2 NM_001282455.1:c.732= NM_001282455.1:c.732C>T NM_001282455.1:c.732C>A
CHRNA2 transcript variant 3 NM_001347705.2:c.300= NM_001347705.2:c.300C>T NM_001347705.2:c.300C>A
CHRNA2 transcript variant 3 NM_001347705.1:c.300= NM_001347705.1:c.300C>T NM_001347705.1:c.300C>A
CHRNA2 transcript variant 5 NM_001347707.2:c.183= NM_001347707.2:c.183C>T NM_001347707.2:c.183C>A
CHRNA2 transcript variant 5 NM_001347707.1:c.183= NM_001347707.1:c.183C>T NM_001347707.1:c.183C>A
CHRNA2 transcript variant 6 NM_001347708.2:c.183= NM_001347708.2:c.183C>T NM_001347708.2:c.183C>A
CHRNA2 transcript variant 6 NM_001347708.1:c.183= NM_001347708.1:c.183C>T NM_001347708.1:c.183C>A
CHRNA2 transcript variant X1 XM_011544389.2:c.183= XM_011544389.2:c.183C>T XM_011544389.2:c.183C>A
neuronal acetylcholine receptor subunit alpha-2 isoform 1 precursor NP_000733.2:p.Phe259= NP_000733.2:p.Phe259= NP_000733.2:p.Phe259Leu
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334635.1:p.Phe100= NP_001334635.1:p.Phe100= NP_001334635.1:p.Phe100Leu
neuronal acetylcholine receptor subunit alpha-2 isoform 2 precursor NP_001269384.1:p.Phe244= NP_001269384.1:p.Phe244= NP_001269384.1:p.Phe244Leu
neuronal acetylcholine receptor subunit alpha-2 isoform 3 NP_001334634.1:p.Phe100= NP_001334634.1:p.Phe100= NP_001334634.1:p.Phe100Leu
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334636.1:p.Phe61= NP_001334636.1:p.Phe61= NP_001334636.1:p.Phe61Leu
neuronal acetylcholine receptor subunit alpha-2 isoform 4 NP_001334637.1:p.Phe61= NP_001334637.1:p.Phe61= NP_001334637.1:p.Phe61Leu
neuronal acetylcholine receptor subunit alpha-2 isoform X1 XP_011542691.1:p.Phe61= XP_011542691.1:p.Phe61= XP_011542691.1:p.Phe61Leu
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#.

14 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss161151684 Dec 01, 2009 (131)
2 NHLBI-ESP ss712834832 Apr 25, 2013 (138)
3 EVA_EXAC ss1689143426 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2301783586 Dec 20, 2016 (150)
5 TOPMED ss2471440443 Dec 20, 2016 (150)
6 GNOMAD ss2737071311 Nov 08, 2017 (151)
7 GNOMAD ss2748023060 Nov 08, 2017 (151)
8 GNOMAD ss2864754035 Nov 08, 2017 (151)
9 TOPMED ss3557398139 Nov 08, 2017 (151)
10 EVA ss3767793413 Jul 13, 2019 (153)
11 EVA ss3824358557 Apr 26, 2020 (154)
12 TOPMED ss4780089179 Apr 26, 2021 (155)
13 TOPMED ss4780089180 Apr 26, 2021 (155)
14 TOMMO_GENOMICS ss5187917166 Apr 26, 2021 (155)
15 ExAC NC_000008.10 - 27321183 Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000008.11 - 27463666 Apr 26, 2021 (155)
17 gnomAD - Exomes NC_000008.10 - 27321183 Jul 13, 2019 (153)
18 GO Exome Sequencing Project NC_000008.10 - 27321183 Oct 12, 2018 (152)
19 8.3KJPN NC_000008.10 - 27321183 Apr 26, 2021 (155)
20 TopMed

Submission ignored due to conflicting rows:
Row 617466739 (NC_000008.11:27463665:G:A 15/264690)
Row 617466740 (NC_000008.11:27463665:G:T 1/264690)

- Apr 26, 2021 (155)
21 TopMed

Submission ignored due to conflicting rows:
Row 617466739 (NC_000008.11:27463665:G:A 15/264690)
Row 617466740 (NC_000008.11:27463665:G:T 1/264690)

- Apr 26, 2021 (155)
22 ALFA NC_000008.11 - 27463666 Apr 26, 2021 (155)
23 ClinVar RCV000608557.1 Oct 12, 2018 (152)
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
9239249, 6241269, 816403, 45886473, ss712834832, ss1689143426, ss2471440443, ss2737071311, ss2748023060, ss2864754035, ss3767793413, ss3824358557, ss5187917166 NC_000008.10:27321182:G:A NC_000008.11:27463665:G:A (self)
RCV000608557.1, 290884981, 385907299, 3960928774, ss2301783586, ss3557398139, ss4780089179 NC_000008.11:27463665:G:A NC_000008.11:27463665:G:A (self)
ss161151684 NT_167187.1:15179328:G:A NC_000008.11:27463665:G:A (self)
3960928774, ss4780089180 NC_000008.11:27463665:G:T NC_000008.11:27463665:G:T
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 rs77769511

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