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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.

rs79646221

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:154571518 (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=0.000036 (5/140088, GnomAD)
A=0.000016 (2/121374, ExAC)
A=0.00000 (0/78698, PAGE_STUDY) (+ 1 more)
A=0.00003 (1/35922, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNB2 : 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 1 NC_000001.11:g.154571518G>A
GRCh38.p13 chr 1 NC_000001.11:g.154571518G>T
GRCh37.p13 chr 1 NC_000001.10:g.154543994G>A
GRCh37.p13 chr 1 NC_000001.10:g.154543994G>T
CHRNB2 RefSeqGene NG_008027.1:g.8738G>A
CHRNB2 RefSeqGene NG_008027.1:g.8738G>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.695G>A R [CGC] > H [CAC] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Arg232His R (Arg) > H (His) Missense Variant
CHRNB2 transcript NM_000748.3:c.695G>T R [CGC] > L [CTC] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Arg232Leu R (Arg) > L (Leu) Missense Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.185G>A R [CGC] > H [CAC] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Arg62His R (Arg) > H (His) Missense Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.185G>T R [CGC] > L [CTC] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Arg62Leu R (Arg) > L (Leu) Missense Variant
CHRNB2 transcript variant X1 XR_001736952.2:n.947G>A N/A Non Coding Transcript Variant
CHRNB2 transcript variant X1 XR_001736952.2:n.947G>T N/A Non Coding 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: A (allele ID: 201036 )
ClinVar Accession Disease Names Clinical Significance
RCV000186991.1 not provided Uncertain-Significance
RCV001347661.1 Autosomal dominant nocturnal frontal lobe epilepsy Uncertain-Significance

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 35922 G=0.99997 A=0.00003
European Sub 26538 G=0.99996 A=0.00004
African Sub 3352 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 3238 G=1.0000 A=0.0000
Asian Sub 146 G=1.000 A=0.000
East Asian Sub 120 G=1.000 A=0.000
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 496 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 4658 G=1.0000 A=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 - Genomes Global Study-wide 140088 G=0.999964 A=0.000036
gnomAD - Genomes European Sub 75864 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 41972 G=0.99993 A=0.00007
gnomAD - Genomes American Sub 13646 G=0.99993 A=0.00007
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 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 121374 G=0.999984 A=0.000016
ExAC Europe Sub 73332 G=0.99997 A=0.00003
ExAC Asian Sub 25164 G=1.00000 A=0.00000
ExAC American Sub 11574 G=1.00000 A=0.00000
ExAC African Sub 10400 G=1.00000 A=0.00000
ExAC Other Sub 904 G=1.000 A=0.000
The PAGE Study Global Study-wide 78698 G=1.00000 A=0.00000
The PAGE Study AfricanAmerican Sub 32514 G=1.00000 A=0.00000
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4532 G=1.0000 A=0.0000
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=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
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 1 NC_000001.11:g.154571518= NC_000001.11:g.154571518G>A NC_000001.11:g.154571518G>T
GRCh37.p13 chr 1 NC_000001.10:g.154543994= NC_000001.10:g.154543994G>A NC_000001.10:g.154543994G>T
CHRNB2 RefSeqGene NG_008027.1:g.8738= NG_008027.1:g.8738G>A NG_008027.1:g.8738G>T
CHRNB2 transcript NM_000748.3:c.695= NM_000748.3:c.695G>A NM_000748.3:c.695G>T
CHRNB2 transcript NM_000748.2:c.695= NM_000748.2:c.695G>A NM_000748.2:c.695G>T
CHRNB2 transcript variant X2 XM_017000180.2:c.185= XM_017000180.2:c.185G>A XM_017000180.2:c.185G>T
CHRNB2 transcript variant X1 XR_001736952.2:n.947= XR_001736952.2:n.947G>A XR_001736952.2:n.947G>T
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Arg232= NP_000739.1:p.Arg232His NP_000739.1:p.Arg232Leu
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Arg62= XP_016855669.1:p.Arg62His XP_016855669.1:p.Arg62Leu
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#.

13 SubSNP, 6 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss161151675 Dec 01, 2009 (131)
2 GSK-GENETICS ss491235468 May 04, 2012 (137)
3 EVA_EXAC ss1685805668 Apr 01, 2015 (144)
4 ILLUMINA ss1958317561 Feb 12, 2016 (147)
5 GNOMAD ss2731893057 Nov 08, 2017 (151)
6 GNOMAD ss2746450877 Nov 08, 2017 (151)
7 GNOMAD ss2761315274 Nov 08, 2017 (151)
8 ILLUMINA ss3021136256 Nov 08, 2017 (151)
9 TOPMED ss3092141398 Nov 08, 2017 (151)
10 ILLUMINA ss3651470500 Oct 11, 2018 (152)
11 ILLUMINA ss3725065362 Jul 12, 2019 (153)
12 PAGE_CC ss3770840924 Jul 12, 2019 (153)
13 EVA ss5236873681 Apr 25, 2021 (155)
14 ExAC NC_000001.10 - 154543994 Oct 11, 2018 (152)
15 gnomAD - Genomes NC_000001.11 - 154571518 Apr 25, 2021 (155)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 915484 (NC_000001.10:154543993:G:G 251061/251064, NC_000001.10:154543993:G:A 3/251064)
Row 915485 (NC_000001.10:154543993:G:G 251062/251064, NC_000001.10:154543993:G:T 2/251064)

- Jul 12, 2019 (153)
17 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 915484 (NC_000001.10:154543993:G:G 251061/251064, NC_000001.10:154543993:G:A 3/251064)
Row 915485 (NC_000001.10:154543993:G:G 251062/251064, NC_000001.10:154543993:G:T 2/251064)

- Jul 12, 2019 (153)
18 The PAGE Study NC_000001.11 - 154571518 Jul 12, 2019 (153)
19 ALFA NC_000001.11 - 154571518 Apr 25, 2021 (155)
20 ClinVar RCV000186991.1 Oct 11, 2018 (152)
21 ClinVar RCV001347661.1 Apr 25, 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
ss491235468 NC_000001.9:152810617:G:A NC_000001.11:154571517:G:A (self)
5024356, ss1685805668, ss1958317561, ss2731893057, ss2746450877, ss2761315274, ss3021136256, ss3651470500 NC_000001.10:154543993:G:A NC_000001.11:154571517:G:A (self)
RCV000186991.1, RCV001347661.1, 27049488, 62393, 20030956, 9756826204, ss3092141398, ss3725065362, ss3770840924, ss5236873681 NC_000001.11:154571517:G:A NC_000001.11:154571517:G:A (self)
ss161151675 NT_004487.19:6032635:G:A NC_000001.11:154571517:G:A (self)
ss2731893057 NC_000001.10:154543993:G:T NC_000001.11:154571517:G: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 rs79646221

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