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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.

rs80342906

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:42765146 (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
C=0.000286 (72/251466, GnomAD_exome)
C=0.000313 (38/121404, ExAC)
C=0.00027 (12/44772, ALFA) (+ 6 more)
C=0.00038 (5/13006, GO-ESP)
C=0.0003 (1/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
C=0.003 (3/998, GoNL)
C=0.007 (4/600, NorthernSweden)
C=0.003 (1/304, FINRISK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHRNA6 : 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.42765146G>A
GRCh38.p13 chr 8 NC_000008.11:g.42765146G>C
GRCh37.p13 chr 8 NC_000008.10:g.42620289G>A
GRCh37.p13 chr 8 NC_000008.10:g.42620289G>C
Gene: CHRNA6, cholinergic receptor nicotinic alpha 6 subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNA6 transcript variant 1 NM_004198.3:c.138C>T N [AAC] > N [AAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-6 isoform 1 precursor NP_004189.1:p.Asn46= N (Asn) > N (Asn) Synonymous Variant
CHRNA6 transcript variant 1 NM_004198.3:c.138C>G N [AAC] > K [AAG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-6 isoform 1 precursor NP_004189.1:p.Asn46Lys N (Asn) > K (Lys) Missense Variant
CHRNA6 transcript variant 2 NM_001199279.1:c.138C>T N [AAC] > N [AAT] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-6 isoform 2 precursor NP_001186208.1:p.Asn46= N (Asn) > N (Asn) Synonymous Variant
CHRNA6 transcript variant 2 NM_001199279.1:c.138C>G N [AAC] > K [AAG] Coding Sequence Variant
neuronal acetylcholine receptor subunit alpha-6 isoform 2 precursor NP_001186208.1:p.Asn46Lys N (Asn) > K (Lys) 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.

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 44772 G=0.99973 A=0.00000, C=0.00027
European Sub 32770 G=0.99966 A=0.00000, C=0.00034
African Sub 3556 G=1.0000 A=0.0000, C=0.0000
African Others Sub 122 G=1.000 A=0.000, C=0.000
African American Sub 3434 G=1.0000 A=0.0000, C=0.0000
Asian Sub 168 G=1.000 A=0.000, C=0.000
East Asian Sub 112 G=1.000 A=0.000, C=0.000
Other Asian Sub 56 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 500 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 628 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 7052 G=0.9999 A=0.0000, C=0.0001


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 251466 G=0.999714 C=0.000286
gnomAD - Exomes European Sub 135390 G=0.999498 C=0.000502
gnomAD - Exomes Asian Sub 49010 G=1.00000 C=0.00000
gnomAD - Exomes American Sub 34592 G=1.00000 C=0.00000
gnomAD - Exomes African Sub 16256 G=0.99988 C=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6138 G=0.9997 C=0.0003
ExAC Global Study-wide 121404 G=0.999687 C=0.000313
ExAC Europe Sub 73346 G=0.99950 C=0.00050
ExAC Asian Sub 25166 G=1.00000 C=0.00000
ExAC American Sub 11578 G=1.00000 C=0.00000
ExAC African Sub 10406 G=0.99990 C=0.00010
ExAC Other Sub 908 G=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99962 C=0.00038
GO Exome Sequencing Project European American Sub 8600 G=0.9995 C=0.0005
GO Exome Sequencing Project African American Sub 4406 G=0.9998 C=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 C=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 C=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.997 C=0.003
Northern Sweden ACPOP Study-wide 600 G=0.993 C=0.007
FINRISK Finnish from FINRISK project Study-wide 304 G=0.997 C=0.003
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.42765146= NC_000008.11:g.42765146G>A NC_000008.11:g.42765146G>C
GRCh37.p13 chr 8 NC_000008.10:g.42620289= NC_000008.10:g.42620289G>A NC_000008.10:g.42620289G>C
CHRNA6 transcript variant 1 NM_004198.3:c.138= NM_004198.3:c.138C>T NM_004198.3:c.138C>G
CHRNA6 transcript variant 2 NM_001199279.1:c.138= NM_001199279.1:c.138C>T NM_001199279.1:c.138C>G
neuronal acetylcholine receptor subunit alpha-6 isoform 1 precursor NP_004189.1:p.Asn46= NP_004189.1:p.Asn46= NP_004189.1:p.Asn46Lys
neuronal acetylcholine receptor subunit alpha-6 isoform 2 precursor NP_001186208.1:p.Asn46= NP_001186208.1:p.Asn46= NP_001186208.1:p.Asn46Lys
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#.

30 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss161151695 Dec 01, 2009 (131)
2 NHLBI-ESP ss342258082 May 09, 2011 (134)
3 GSK-GENETICS ss491277450 May 04, 2012 (137)
4 EXOME_CHIP ss491413106 May 04, 2012 (137)
5 GOLDSTEINLAB ss507868984 May 04, 2012 (137)
6 EVA-GONL ss985447549 Aug 21, 2014 (142)
7 EVA_FINRISK ss1584058319 Apr 01, 2015 (144)
8 EVA_DECODE ss1595045141 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1620495317 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1663489350 Apr 01, 2015 (144)
11 EVA_EXAC ss1689185120 Apr 01, 2015 (144)
12 HUMAN_LONGEVITY ss2302699694 Dec 20, 2016 (150)
13 TOPMED ss2472356641 Dec 20, 2016 (150)
14 GNOMAD ss2737137119 Nov 08, 2017 (151)
15 GNOMAD ss2748042673 Nov 08, 2017 (151)
16 GNOMAD ss2865991649 Nov 08, 2017 (151)
17 AFFY ss2985437790 Nov 08, 2017 (151)
18 AFFY ss2986081610 Nov 08, 2017 (151)
19 SWEGEN ss3003069218 Nov 08, 2017 (151)
20 ILLUMINA ss3022841379 Nov 08, 2017 (151)
21 TOPMED ss3560238693 Nov 08, 2017 (151)
22 TOPMED ss3560238694 Nov 08, 2017 (151)
23 ILLUMINA ss3653383055 Oct 12, 2018 (152)
24 ILLUMINA ss3654200016 Oct 12, 2018 (152)
25 EVA_DECODE ss3721892191 Jul 13, 2019 (153)
26 ILLUMINA ss3726534072 Jul 13, 2019 (153)
27 ACPOP ss3735611484 Jul 13, 2019 (153)
28 EVA ss3824367625 Apr 26, 2020 (154)
29 TOPMED ss4783806391 Apr 26, 2021 (155)
30 TOPMED ss4783806392 Apr 26, 2021 (155)
31 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 42620289 Oct 12, 2018 (152)
32 ExAC NC_000008.10 - 42620289 Oct 12, 2018 (152)
33 FINRISK NC_000008.10 - 42620289 Apr 26, 2020 (154)
34 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 294051354 (NC_000008.11:42765145:G:A 1/140270)
Row 294051355 (NC_000008.11:42765145:G:C 56/140270)

- Apr 26, 2021 (155)
35 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 294051354 (NC_000008.11:42765145:G:A 1/140270)
Row 294051355 (NC_000008.11:42765145:G:C 56/140270)

- Apr 26, 2021 (155)
36 gnomAD - Exomes NC_000008.10 - 42620289 Jul 13, 2019 (153)
37 GO Exome Sequencing Project NC_000008.10 - 42620289 Oct 12, 2018 (152)
38 Genome of the Netherlands Release 5 NC_000008.10 - 42620289 Apr 26, 2020 (154)
39 Northern Sweden NC_000008.10 - 42620289 Jul 13, 2019 (153)
40 TopMed

Submission ignored due to conflicting rows:
Row 621183951 (NC_000008.11:42765145:G:A 1/264690)
Row 621183952 (NC_000008.11:42765145:G:C 60/264690)

- Apr 26, 2021 (155)
41 TopMed

Submission ignored due to conflicting rows:
Row 621183951 (NC_000008.11:42765145:G:A 1/264690)
Row 621183952 (NC_000008.11:42765145:G:C 60/264690)

- Apr 26, 2021 (155)
42 UK 10K study - Twins NC_000008.10 - 42620289 Oct 12, 2018 (152)
43 ALFA NC_000008.11 - 42765146 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
388200045, 12814101477, ss3560238693, ss4783806391 NC_000008.11:42765145:G:A NC_000008.11:42765145:G:A (self)
ss491277450, ss507868984, ss1595045141 NC_000008.9:42739445:G:C NC_000008.11:42765145:G:C (self)
23193044, 9284232, 54780, 6308705, 825472, 10357356, 8896349, 23193044, ss342258082, ss491413106, ss985447549, ss1584058319, ss1620495317, ss1663489350, ss1689185120, ss2472356641, ss2737137119, ss2748042673, ss2865991649, ss2985437790, ss2986081610, ss3003069218, ss3022841379, ss3653383055, ss3654200016, ss3735611484, ss3824367625 NC_000008.10:42620288:G:C NC_000008.11:42765145:G:C (self)
388200045, 12814101477, ss2302699694, ss3560238694, ss3721892191, ss3726534072, ss4783806392 NC_000008.11:42765145:G:C NC_000008.11:42765145:G:C (self)
ss161151695 NT_167187.1:30478434:G:C NC_000008.11:42765145: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 rs80342906

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