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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.

rs78682427

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:42736490 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000147 (39/264690, TOPMED)
T=0.000154 (29/188086, ALFA)
T=0.000143 (20/140242, GnomAD) (+ 5 more)
T=0.000091 (11/121390, ExAC)
T=0.00005 (4/78698, PAGE_STUDY)
T=0.00015 (2/13006, GO-ESP)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHRNB3 : Stop Gained
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.42736490C>G
GRCh38.p13 chr 8 NC_000008.11:g.42736490C>T
GRCh37.p13 chr 8 NC_000008.10:g.42591633C>G
GRCh37.p13 chr 8 NC_000008.10:g.42591633C>T
Gene: CHRNB3, cholinergic receptor nicotinic beta 3 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB3 transcript variant 1 NM_000749.5:c.1249C>G Q [CAA] > E [GAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform 1 precursor NP_000740.1:p.Gln417Glu Q (Gln) > E (Glu) Missense Variant
CHRNB3 transcript variant 1 NM_000749.5:c.1249C>T Q [CAA] > * [TAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform 1 precursor NP_000740.1:p.Gln417Ter Q (Gln) > * (Ter) Stop Gained
CHRNB3 transcript variant 2 NM_001347717.2:c.1027C>G Q [CAA] > E [GAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform 2 NP_001334646.1:p.Gln343Glu Q (Gln) > E (Glu) Missense Variant
CHRNB3 transcript variant 2 NM_001347717.2:c.1027C>T Q [CAA] > * [TAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform 2 NP_001334646.1:p.Gln343Ter Q (Gln) > * (Ter) Stop Gained
CHRNB3 transcript variant X1 XM_011544390.2:c.862C>G Q [CAA] > E [GAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform X1 XP_011542692.1:p.Gln288Glu Q (Gln) > E (Glu) Missense Variant
CHRNB3 transcript variant X1 XM_011544390.2:c.862C>T Q [CAA] > * [TAA] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-3 isoform X1 XP_011542692.1:p.Gln288Ter Q (Gln) > * (Ter) Stop Gained
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 188086 C=0.999846 T=0.000154
European Sub 163784 C=0.999835 T=0.000165
African Sub 4952 C=0.9998 T=0.0002
African Others Sub 176 C=1.000 T=0.000
African American Sub 4776 C=0.9998 T=0.0002
Asian Sub 3394 C=1.0000 T=0.0000
East Asian Sub 2712 C=1.0000 T=0.0000
Other Asian Sub 682 C=1.000 T=0.000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 966 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 13914 C=0.99993 T=0.00007


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 C=0.999853 T=0.000147
gnomAD - Genomes Global Study-wide 140242 C=0.999857 T=0.000143
gnomAD - Genomes European Sub 75942 C=0.99982 T=0.00018
gnomAD - Genomes African Sub 42042 C=0.99988 T=0.00012
gnomAD - Genomes American Sub 13650 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9995 T=0.0005
ExAC Global Study-wide 121390 C=0.999909 T=0.000091
ExAC Europe Sub 73338 C=0.99986 T=0.00014
ExAC Asian Sub 25162 C=1.00000 T=0.00000
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10404 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
The PAGE Study Global Study-wide 78698 C=0.99995 T=0.00005
The PAGE Study AfricanAmerican Sub 32514 C=0.99988 T=0.00012
The PAGE Study Mexican Sub 10808 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99985 T=0.00015
GO Exome Sequencing Project European American Sub 8600 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=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 C= G T
GRCh38.p13 chr 8 NC_000008.11:g.42736490= NC_000008.11:g.42736490C>G NC_000008.11:g.42736490C>T
GRCh37.p13 chr 8 NC_000008.10:g.42591633= NC_000008.10:g.42591633C>G NC_000008.10:g.42591633C>T
CHRNB3 transcript variant 1 NM_000749.5:c.1249= NM_000749.5:c.1249C>G NM_000749.5:c.1249C>T
CHRNB3 transcript variant 1 NM_000749.4:c.1249= NM_000749.4:c.1249C>G NM_000749.4:c.1249C>T
CHRNB3 transcript NM_000749.3:c.1249= NM_000749.3:c.1249C>G NM_000749.3:c.1249C>T
CHRNB3 transcript variant 2 NM_001347717.2:c.1027= NM_001347717.2:c.1027C>G NM_001347717.2:c.1027C>T
CHRNB3 transcript variant 2 NM_001347717.1:c.1027= NM_001347717.1:c.1027C>G NM_001347717.1:c.1027C>T
CHRNB3 transcript variant X1 XM_011544390.2:c.862= XM_011544390.2:c.862C>G XM_011544390.2:c.862C>T
neuronal acetylcholine receptor subunit beta-3 isoform 1 precursor NP_000740.1:p.Gln417= NP_000740.1:p.Gln417Glu NP_000740.1:p.Gln417Ter
neuronal acetylcholine receptor subunit beta-3 isoform 2 NP_001334646.1:p.Gln343= NP_001334646.1:p.Gln343Glu NP_001334646.1:p.Gln343Ter
neuronal acetylcholine receptor subunit beta-3 isoform X1 XP_011542692.1:p.Gln288= XP_011542692.1:p.Gln288Glu XP_011542692.1:p.Gln288Ter
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#.

39 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss161151691 Dec 01, 2009 (131)
2 EXOME_CHIP ss491413092 May 04, 2012 (137)
3 CLINSEQ_SNP ss491924637 May 04, 2012 (137)
4 GOLDSTEINLAB ss507877749 May 04, 2012 (137)
5 NHLBI-ESP ss712842203 Apr 25, 2013 (138)
6 ILLUMINA ss780869697 Sep 08, 2015 (146)
7 ILLUMINA ss783554727 Sep 08, 2015 (146)
8 EVA_UK10K_ALSPAC ss1620494849 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1663488882 Apr 01, 2015 (144)
10 EVA_EXAC ss1689184789 Apr 01, 2015 (144)
11 ILLUMINA ss1752732684 Sep 08, 2015 (146)
12 ILLUMINA ss1917828274 Feb 12, 2016 (147)
13 ILLUMINA ss1946235867 Feb 12, 2016 (147)
14 ILLUMINA ss1946235868 Feb 12, 2016 (147)
15 ILLUMINA ss1959106940 Feb 12, 2016 (147)
16 ILLUMINA ss1959106941 Feb 12, 2016 (147)
17 HUMAN_LONGEVITY ss2302697927 Dec 20, 2016 (150)
18 TOPMED ss2472354905 Dec 20, 2016 (150)
19 GNOMAD ss2737136644 Nov 08, 2017 (151)
20 GNOMAD ss2748042536 Nov 08, 2017 (151)
21 GNOMAD ss2865989275 Nov 08, 2017 (151)
22 AFFY ss2986081537 Nov 08, 2017 (151)
23 ILLUMINA ss3022841323 Nov 08, 2017 (151)
24 TOPMED ss3560233245 Nov 08, 2017 (151)
25 ILLUMINA ss3625951010 Oct 12, 2018 (152)
26 ILLUMINA ss3630049865 Oct 12, 2018 (152)
27 ILLUMINA ss3635169800 Oct 12, 2018 (152)
28 ILLUMINA ss3640877090 Oct 12, 2018 (152)
29 ILLUMINA ss3644969071 Oct 12, 2018 (152)
30 ILLUMINA ss3644969072 Oct 12, 2018 (152)
31 ILLUMINA ss3653382999 Oct 12, 2018 (152)
32 ILLUMINA ss3726534019 Jul 13, 2019 (153)
33 ILLUMINA ss3744305241 Jul 13, 2019 (153)
34 ILLUMINA ss3744579803 Jul 13, 2019 (153)
35 ILLUMINA ss3745469673 Jul 13, 2019 (153)
36 PAGE_CC ss3771439516 Jul 13, 2019 (153)
37 ILLUMINA ss3772962124 Jul 13, 2019 (153)
38 EVA ss3824367547 Apr 26, 2020 (154)
39 TOPMED ss4783799462 Apr 26, 2021 (155)
40 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 42591633 Oct 12, 2018 (152)
41 ExAC NC_000008.10 - 42591633 Oct 12, 2018 (152)
42 gnomAD - Genomes NC_000008.11 - 42736490 Apr 26, 2021 (155)
43 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6308175 (NC_000008.10:42591632:C:C 251321/251322, NC_000008.10:42591632:C:G 1/251322)
Row 6308176 (NC_000008.10:42591632:C:C 251300/251322, NC_000008.10:42591632:C:T 22/251322)

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

Submission ignored due to conflicting rows:
Row 6308175 (NC_000008.10:42591632:C:C 251321/251322, NC_000008.10:42591632:C:G 1/251322)
Row 6308176 (NC_000008.10:42591632:C:C 251300/251322, NC_000008.10:42591632:C:T 22/251322)

- Jul 13, 2019 (153)
45 GO Exome Sequencing Project NC_000008.10 - 42591633 Oct 12, 2018 (152)
46 The PAGE Study NC_000008.11 - 42736490 Jul 13, 2019 (153)
47 TopMed NC_000008.11 - 42736490 Apr 26, 2021 (155)
48 UK 10K study - Twins NC_000008.10 - 42591633 Oct 12, 2018 (152)
49 ALFA NC_000008.11 - 42736490 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
NC_000008.10:42591632:C:G NC_000008.11:42736489:C:G (self)
ss491924637, ss507877749 NC_000008.9:42710789:C:T NC_000008.11:42736489:C:T (self)
23192527, 9283878, 825394, 23192527, ss491413092, ss712842203, ss780869697, ss783554727, ss1620494849, ss1663488882, ss1689184789, ss1752732684, ss1917828274, ss1946235867, ss1946235868, ss1959106940, ss1959106941, ss2472354905, ss2737136644, ss2748042536, ss2865989275, ss2986081537, ss3022841323, ss3625951010, ss3630049865, ss3635169800, ss3640877090, ss3644969071, ss3644969072, ss3653382999, ss3744305241, ss3744579803, ss3745469673, ss3772962124, ss3824367547 NC_000008.10:42591632:C:T NC_000008.11:42736489:C:T (self)
294045367, 660985, 388195716, 621177022, 7930041985, ss2302697927, ss3560233245, ss3726534019, ss3771439516, ss4783799462 NC_000008.11:42736489:C:T NC_000008.11:42736489:C:T (self)
ss161151691 NT_167187.1:30449778:C:T NC_000008.11:42736489:C:T (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 rs78682427

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