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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.

rs71651692

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:154569474 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000677 (170/251214, GnomAD_exome)
T=0.000682 (139/203690, ALFA)
T=0.000535 (75/140090, GnomAD) (+ 8 more)
T=0.000815 (98/120264, ExAC)
T=0.00010 (8/78694, PAGE_STUDY)
T=0.00062 (8/13006, GO-ESP)
T=0.0002 (1/5008, 1000G)
T=0.0004 (2/4480, Estonian)
T=0.0008 (3/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.001 (1/998, GoNL)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNB2 : Missense Variant
LOC107985206 : 2KB Upstream 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 1 NC_000001.11:g.154569474C>A
GRCh38.p13 chr 1 NC_000001.11:g.154569474C>T
GRCh37.p13 chr 1 NC_000001.10:g.154541950C>A
GRCh37.p13 chr 1 NC_000001.10:g.154541950C>T
CHRNB2 RefSeqGene NG_008027.1:g.6694C>A
CHRNB2 RefSeqGene NG_008027.1:g.6694C>T
Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB2 transcript NM_000748.3:c.77C>A T [ACG] > K [AAG] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Thr26Lys T (Thr) > K (Lys) Missense Variant
CHRNB2 transcript NM_000748.3:c.77C>T T [ACG] > M [ATG] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Thr26Met T (Thr) > M (Met) Missense Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.-298= N/A 5 Prime UTR Variant
CHRNB2 transcript variant X1 XR_001736952.2:n.329C>A N/A Non Coding Transcript Variant
CHRNB2 transcript variant X1 XR_001736952.2:n.329C>T N/A Non Coding Transcript Variant
Gene: LOC107985206, uncharacterized LOC107985206 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107985206 transcript variant X1 XR_001738237.1:n. N/A Upstream Transcript Variant
LOC107985206 transcript variant X2 XR_001738238.2:n. N/A Upstream Transcript 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: T (allele ID: 201024 )
ClinVar Accession Disease Names Clinical Significance
RCV000186981.5 not specified Benign-Likely-Benign
RCV000531578.4 Autosomal dominant nocturnal frontal lobe epilepsy Likely-Benign
RCV000717241.1 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 203690 C=0.999318 A=0.000000, T=0.000682
European Sub 174352 C=0.999266 A=0.000000, T=0.000734
African Sub 4952 C=1.0000 A=0.0000, T=0.0000
African Others Sub 176 C=1.000 A=0.000, T=0.000
African American Sub 4776 C=1.0000 A=0.0000, T=0.0000
Asian Sub 6344 C=1.0000 A=0.0000, T=0.0000
East Asian Sub 4498 C=1.0000 A=0.0000, T=0.0000
Other Asian Sub 1846 C=1.0000 A=0.0000, T=0.0000
Latin American 1 Sub 796 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 968 C=1.000 A=0.000, T=0.000
South Asian Sub 280 C=1.000 A=0.000, T=0.000
Other Sub 15998 C=0.99931 A=0.00000, T=0.00069


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 251214 C=0.999323 T=0.000677
gnomAD - Exomes European Sub 135224 C=0.999009 T=0.000991
gnomAD - Exomes Asian Sub 48974 C=0.99957 T=0.00043
gnomAD - Exomes American Sub 34562 C=0.99968 T=0.00032
gnomAD - Exomes African Sub 16244 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 C=0.9993 T=0.0007
gnomAD - Genomes Global Study-wide 140090 C=0.999465 T=0.000535
gnomAD - Genomes European Sub 75892 C=0.99914 T=0.00086
gnomAD - Genomes African Sub 41950 C=0.99986 T=0.00014
gnomAD - Genomes American Sub 13642 C=0.99985 T=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9991 T=0.0009
ExAC Global Study-wide 120264 C=0.999185 T=0.000815
ExAC Europe Sub 72788 C=0.99885 T=0.00115
ExAC Asian Sub 24832 C=0.99956 T=0.00044
ExAC American Sub 11456 C=0.99974 T=0.00026
ExAC African Sub 10294 C=1.00000 T=0.00000
ExAC Other Sub 894 C=1.000 T=0.000
The PAGE Study Global Study-wide 78694 C=0.99990 T=0.00010
The PAGE Study AfricanAmerican Sub 32508 C=0.99991 T=0.00009
The PAGE Study Mexican Sub 10810 C=0.99991 T=0.00009
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9999 T=0.0001
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=0.9993 T=0.0007
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=0.99938 T=0.00062
GO Exome Sequencing Project European American Sub 8600 C=0.9991 T=0.0009
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9996 T=0.0004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9992 T=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
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= A T
GRCh38.p13 chr 1 NC_000001.11:g.154569474= NC_000001.11:g.154569474C>A NC_000001.11:g.154569474C>T
GRCh37.p13 chr 1 NC_000001.10:g.154541950= NC_000001.10:g.154541950C>A NC_000001.10:g.154541950C>T
CHRNB2 RefSeqGene NG_008027.1:g.6694= NG_008027.1:g.6694C>A NG_008027.1:g.6694C>T
CHRNB2 transcript NM_000748.3:c.77= NM_000748.3:c.77C>A NM_000748.3:c.77C>T
CHRNB2 transcript NM_000748.2:c.77= NM_000748.2:c.77C>A NM_000748.2:c.77C>T
CHRNB2 transcript variant X2 XM_017000180.2:c.-298= XM_017000180.2:c.-298C>A XM_017000180.2:c.-298C>T
CHRNB2 transcript variant X1 XR_001736952.2:n.329= XR_001736952.2:n.329C>A XR_001736952.2:n.329C>T
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Thr26= NP_000739.1:p.Thr26Lys NP_000739.1:p.Thr26Met
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#.

48 SubSNP, 13 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SHGC ss99307538 Feb 13, 2009 (130)
2 RWHITE ss141045453 Dec 01, 2009 (131)
3 PERLEGEN ss161151680 Dec 01, 2009 (131)
4 NHLBI-ESP ss341996688 May 09, 2011 (134)
5 GSK-GENETICS ss491235419 May 04, 2012 (137)
6 EXOME_CHIP ss491302328 May 04, 2012 (137)
7 CLINSEQ_SNP ss491605068 May 04, 2012 (137)
8 ILLUMINA ss780693649 Sep 08, 2015 (146)
9 ILLUMINA ss783367515 Sep 08, 2015 (146)
10 EVA-GONL ss975682531 Aug 21, 2014 (142)
11 1000GENOMES ss1292925334 Aug 21, 2014 (142)
12 EVA_UK10K_ALSPAC ss1601213834 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1644207867 Apr 01, 2015 (144)
14 EVA_EXAC ss1685805517 Apr 01, 2015 (144)
15 ILLUMINA ss1751872195 Sep 08, 2015 (146)
16 ILLUMINA ss1917735339 Feb 12, 2016 (147)
17 ILLUMINA ss1946009534 Feb 12, 2016 (147)
18 ILLUMINA ss1958317555 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2166540600 Dec 20, 2016 (150)
20 TOPMED ss2329045499 Dec 20, 2016 (150)
21 GNOMAD ss2731892845 Nov 08, 2017 (151)
22 GNOMAD ss2746450826 Nov 08, 2017 (151)
23 GNOMAD ss2761315150 Nov 08, 2017 (151)
24 AFFY ss2984879298 Nov 08, 2017 (151)
25 AFFY ss2985525048 Nov 08, 2017 (151)
26 SWEGEN ss2987752025 Nov 08, 2017 (151)
27 ILLUMINA ss3021136251 Nov 08, 2017 (151)
28 TOPMED ss3092141082 Nov 08, 2017 (151)
29 TOPMED ss3092141083 Nov 08, 2017 (151)
30 ILLUMINA ss3626208381 Oct 11, 2018 (152)
31 ILLUMINA ss3634349869 Oct 11, 2018 (152)
32 ILLUMINA ss3640057226 Oct 11, 2018 (152)
33 ILLUMINA ss3644505493 Oct 11, 2018 (152)
34 ILLUMINA ss3651470495 Oct 11, 2018 (152)
35 ILLUMINA ss3653648493 Oct 11, 2018 (152)
36 EGCUT_WGS ss3655692205 Jul 12, 2019 (153)
37 EVA_DECODE ss3687782233 Jul 12, 2019 (153)
38 ILLUMINA ss3725065357 Jul 12, 2019 (153)
39 ILLUMINA ss3744352569 Jul 12, 2019 (153)
40 ILLUMINA ss3744650778 Jul 12, 2019 (153)
41 EVA ss3746808022 Jul 12, 2019 (153)
42 PAGE_CC ss3770840919 Jul 12, 2019 (153)
43 ILLUMINA ss3772151912 Jul 12, 2019 (153)
44 EVA ss3823663121 Apr 25, 2020 (154)
45 EVA ss3825575792 Apr 25, 2020 (154)
46 TOPMED ss4468299617 Apr 25, 2021 (155)
47 TOPMED ss4468299618 Apr 25, 2021 (155)
48 EVA ss5236873679 Apr 25, 2021 (155)
49 1000Genomes NC_000001.10 - 154541950 Oct 11, 2018 (152)
50 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 154541950 Oct 11, 2018 (152)
51 Genetic variation in the Estonian population NC_000001.10 - 154541950 Oct 11, 2018 (152)
52 ExAC NC_000001.10 - 154541950 Oct 11, 2018 (152)
53 gnomAD - Genomes NC_000001.11 - 154569474 Apr 25, 2021 (155)
54 gnomAD - Exomes NC_000001.10 - 154541950 Jul 12, 2019 (153)
55 GO Exome Sequencing Project NC_000001.10 - 154541950 Oct 11, 2018 (152)
56 Genome of the Netherlands Release 5 NC_000001.10 - 154541950 Apr 25, 2020 (154)
57 The PAGE Study NC_000001.11 - 154569474 Jul 12, 2019 (153)
58 TopMed

Submission ignored due to conflicting rows:
Row 31905952 (NC_000001.11:154569473:C:A 1/264690)
Row 31905953 (NC_000001.11:154569473:C:T 150/264690)

- Apr 25, 2021 (155)
59 TopMed

Submission ignored due to conflicting rows:
Row 31905952 (NC_000001.11:154569473:C:A 1/264690)
Row 31905953 (NC_000001.11:154569473:C:T 150/264690)

- Apr 25, 2021 (155)
60 UK 10K study - Twins NC_000001.10 - 154541950 Oct 11, 2018 (152)
61 ALFA NC_000001.11 - 154569474 Apr 25, 2021 (155)
62 ClinVar RCV000186981.5 Apr 25, 2021 (155)
63 ClinVar RCV000531578.4 Apr 25, 2021 (155)
64 ClinVar RCV000717241.1 Jul 12, 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
20030675, 2552930440, ss3092141082, ss4468299617 NC_000001.11:154569473:C:A NC_000001.11:154569473:C:A (self)
ss491235419, ss491605068 NC_000001.9:152808573:C:T NC_000001.11:154569473:C:T (self)
3717382, 2021058, 1430453, 5024196, 915259, 121719, 878174, 2021058, ss341996688, ss491302328, ss780693649, ss783367515, ss975682531, ss1292925334, ss1601213834, ss1644207867, ss1685805517, ss1751872195, ss1917735339, ss1946009534, ss1958317555, ss2329045499, ss2731892845, ss2746450826, ss2761315150, ss2984879298, ss2985525048, ss2987752025, ss3021136251, ss3626208381, ss3634349869, ss3640057226, ss3644505493, ss3651470495, ss3653648493, ss3655692205, ss3744352569, ss3744650778, ss3746808022, ss3772151912, ss3823663121, ss3825575792 NC_000001.10:154541949:C:T NC_000001.11:154569473:C:T (self)
RCV000186981.5, RCV000531578.4, RCV000717241.1, 27049119, 62388, 20030675, 2552930440, ss2166540600, ss3092141083, ss3687782233, ss3725065357, ss3770840919, ss4468299618, ss5236873679 NC_000001.11:154569473:C:T NC_000001.11:154569473:C:T (self)
ss99307538, ss141045453, ss161151680 NT_004487.19:6030591:C:T NC_000001.11:154569473: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 rs71651692

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