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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs376844505

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:174757590 (GRCh38.p14) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000121 (17/140230, GnomAD)
T=0.000066 (8/121202, ExAC)
T=0.00006 (2/35800, ALFA) (+ 6 more)
T=0.00008 (1/13006, GO-ESP)
T=0.0008 (3/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.002 (1/534, MGP)
T=0.005 (1/214, Vietnamese)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNA1 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 52162 C=0.99994 A=0.00000, G=0.00000, T=0.00006
European Sub 36810 C=0.99995 A=0.00000, G=0.00000, T=0.00005
African Sub 7804 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Others Sub 298 C=1.000 A=0.000, G=0.000, T=0.000
African American Sub 7506 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Asian Sub 112 C=1.000 A=0.000, G=0.000, T=0.000
East Asian Sub 86 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 1 Sub 500 C=1.000 A=0.000, G=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 6210 C=0.9998 A=0.0000, G=0.0000, T=0.0002


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 140230 C=0.999879 T=0.000121
gnomAD - Genomes European Sub 75932 C=0.99987 T=0.00013
gnomAD - Genomes African Sub 42040 C=0.99988 T=0.00012
gnomAD - Genomes American Sub 13654 C=0.99985 T=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
ExAC Global Study-wide 121202 C=0.999934 T=0.000066
ExAC Europe Sub 73270 C=0.99992 T=0.00008
ExAC Asian Sub 25138 C=0.99996 T=0.00004
ExAC American Sub 11560 C=1.00000 T=0.00000
ExAC African Sub 10328 C=0.99990 T=0.00010
ExAC Other Sub 906 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 35800 C=0.99994 A=0.00000, G=0.00000, T=0.00006
Allele Frequency Aggregator European Sub 26720 C=0.99996 A=0.00000, G=0.00000, T=0.00004
Allele Frequency Aggregator Other Sub 4776 C=0.9998 A=0.0000, G=0.0000, T=0.0002
Allele Frequency Aggregator African Sub 2966 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, G=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=0.9999 T=0.0001
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=0.9992 T=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 T=0.0003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.995 T=0.005
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.p14 chr 2 NC_000002.12:g.174757590C>A
GRCh38.p14 chr 2 NC_000002.12:g.174757590C>G
GRCh38.p14 chr 2 NC_000002.12:g.174757590C>T
GRCh37.p13 chr 2 NC_000002.11:g.175622318C>A
GRCh37.p13 chr 2 NC_000002.11:g.175622318C>G
GRCh37.p13 chr 2 NC_000002.11:g.175622318C>T
CHRNA1 RefSeqGene NG_008172.1:g.11883G>T
CHRNA1 RefSeqGene NG_008172.1:g.11883G>C
CHRNA1 RefSeqGene NG_008172.1:g.11883G>A
Gene: CHRNA1, cholinergic receptor nicotinic alpha 1 subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNA1 transcript variant 1 NM_001039523.3:c.395G>T R [CGC] > L [CTC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform a precursor NP_001034612.1:p.Arg132Leu R (Arg) > L (Leu) Missense Variant
CHRNA1 transcript variant 1 NM_001039523.3:c.395G>C R [CGC] > P [CCC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform a precursor NP_001034612.1:p.Arg132Pro R (Arg) > P (Pro) Missense Variant
CHRNA1 transcript variant 1 NM_001039523.3:c.395G>A R [CGC] > H [CAC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform a precursor NP_001034612.1:p.Arg132His R (Arg) > H (His) Missense Variant
CHRNA1 transcript variant 2 NM_000079.4:c.320G>T R [CGC] > L [CTC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform b precursor NP_000070.1:p.Arg107Leu R (Arg) > L (Leu) Missense Variant
CHRNA1 transcript variant 2 NM_000079.4:c.320G>C R [CGC] > P [CCC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform b precursor NP_000070.1:p.Arg107Pro R (Arg) > P (Pro) Missense Variant
CHRNA1 transcript variant 2 NM_000079.4:c.320G>A R [CGC] > H [CAC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform b precursor NP_000070.1:p.Arg107His R (Arg) > H (His) Missense Variant
CHRNA1 transcript variant X1 XM_017003256.2:c.416G>T R [CGC] > L [CTC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X1 XP_016858745.1:p.Arg139Leu R (Arg) > L (Leu) Missense Variant
CHRNA1 transcript variant X1 XM_017003256.2:c.416G>C R [CGC] > P [CCC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X1 XP_016858745.1:p.Arg139Pro R (Arg) > P (Pro) Missense Variant
CHRNA1 transcript variant X1 XM_017003256.2:c.416G>A R [CGC] > H [CAC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X1 XP_016858745.1:p.Arg139His R (Arg) > H (His) Missense Variant
CHRNA1 transcript variant X2 XM_017003257.2:c.341G>T R [CGC] > L [CTC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X2 XP_016858746.1:p.Arg114Leu R (Arg) > L (Leu) Missense Variant
CHRNA1 transcript variant X2 XM_017003257.2:c.341G>C R [CGC] > P [CCC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X2 XP_016858746.1:p.Arg114Pro R (Arg) > P (Pro) Missense Variant
CHRNA1 transcript variant X2 XM_017003257.2:c.341G>A R [CGC] > H [CAC] Coding Sequence Variant
acetylcholine receptor subunit alpha isoform X2 XP_016858746.1:p.Arg114His R (Arg) > H (His) 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: 265903 )
ClinVar Accession Disease Names Clinical Significance
RCV000387156.3 not provided Uncertain-Significance
RCV001313199.4 Lethal multiple pterygium syndrome Uncertain-Significance
Allele: T (allele ID: 516746 )
ClinVar Accession Disease Names Clinical Significance
RCV000642108.6 Lethal multiple pterygium syndrome Uncertain-Significance
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 G T
GRCh38.p14 chr 2 NC_000002.12:g.174757590= NC_000002.12:g.174757590C>A NC_000002.12:g.174757590C>G NC_000002.12:g.174757590C>T
GRCh37.p13 chr 2 NC_000002.11:g.175622318= NC_000002.11:g.175622318C>A NC_000002.11:g.175622318C>G NC_000002.11:g.175622318C>T
CHRNA1 RefSeqGene NG_008172.1:g.11883= NG_008172.1:g.11883G>T NG_008172.1:g.11883G>C NG_008172.1:g.11883G>A
CHRNA1 transcript variant 2 NM_000079.4:c.320= NM_000079.4:c.320G>T NM_000079.4:c.320G>C NM_000079.4:c.320G>A
CHRNA1 transcript variant 2 NM_000079.3:c.320= NM_000079.3:c.320G>T NM_000079.3:c.320G>C NM_000079.3:c.320G>A
CHRNA1 transcript variant 1 NM_001039523.3:c.395= NM_001039523.3:c.395G>T NM_001039523.3:c.395G>C NM_001039523.3:c.395G>A
CHRNA1 transcript variant 1 NM_001039523.2:c.395= NM_001039523.2:c.395G>T NM_001039523.2:c.395G>C NM_001039523.2:c.395G>A
CHRNA1 transcript variant X1 XM_017003256.2:c.416= XM_017003256.2:c.416G>T XM_017003256.2:c.416G>C XM_017003256.2:c.416G>A
CHRNA1 transcript variant X1 XM_017003256.1:c.416= XM_017003256.1:c.416G>T XM_017003256.1:c.416G>C XM_017003256.1:c.416G>A
CHRNA1 transcript variant X2 XM_017003257.2:c.341= XM_017003257.2:c.341G>T XM_017003257.2:c.341G>C XM_017003257.2:c.341G>A
CHRNA1 transcript variant X2 XM_017003257.1:c.341= XM_017003257.1:c.341G>T XM_017003257.1:c.341G>C XM_017003257.1:c.341G>A
acetylcholine receptor subunit alpha isoform b precursor NP_000070.1:p.Arg107= NP_000070.1:p.Arg107Leu NP_000070.1:p.Arg107Pro NP_000070.1:p.Arg107His
acetylcholine receptor subunit alpha isoform a precursor NP_001034612.1:p.Arg132= NP_001034612.1:p.Arg132Leu NP_001034612.1:p.Arg132Pro NP_001034612.1:p.Arg132His
acetylcholine receptor subunit alpha isoform X1 XP_016858745.1:p.Arg139= XP_016858745.1:p.Arg139Leu XP_016858745.1:p.Arg139Pro XP_016858745.1:p.Arg139His
acetylcholine receptor subunit alpha isoform X2 XP_016858746.1:p.Arg114= XP_016858746.1:p.Arg114Leu XP_016858746.1:p.Arg114Pro XP_016858746.1:p.Arg114His
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#.

18 SubSNP, 13 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712467400 Apr 25, 2013 (138)
2 EVA_UK10K_ALSPAC ss1605196572 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1648190605 Apr 01, 2015 (144)
4 EVA_EXAC ss1686604540 Apr 01, 2015 (144)
5 EVA_MGP ss1710987819 Apr 01, 2015 (144)
6 CLINVAR ss2136848028 Dec 04, 2016 (149)
7 HUMAN_LONGEVITY ss2236762244 Dec 20, 2016 (150)
8 GNOMAD ss2733126796 Nov 08, 2017 (151)
9 GNOMAD ss2746820148 Nov 08, 2017 (151)
10 GNOMAD ss2783073798 Nov 08, 2017 (151)
11 EVA_DECODE ss3705471914 Jul 13, 2019 (153)
12 KHV_HUMAN_GENOMES ss3802107551 Jul 13, 2019 (153)
13 EVA ss3823828105 Apr 25, 2020 (154)
14 KRGDB ss3899665440 Apr 25, 2020 (154)
15 TOPMED ss4534515161 Apr 26, 2021 (155)
16 TOPMED ss4534515162 Apr 26, 2021 (155)
17 HUGCELL_USP ss5450761542 Oct 12, 2022 (156)
18 EVA ss5956629141 Oct 12, 2022 (156)
19 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 175622318 Oct 11, 2018 (152)
20 ExAC NC_000002.11 - 175622318 Oct 11, 2018 (152)
21 gnomAD - Genomes NC_000002.12 - 174757590 Apr 26, 2021 (155)
22 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2186984 (NC_000002.11:175622317:C:C 251375/251376, NC_000002.11:175622317:C:A 1/251376)
Row 2186985 (NC_000002.11:175622317:C:C 251362/251376, NC_000002.11:175622317:C:T 14/251376)

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

Submission ignored due to conflicting rows:
Row 2186984 (NC_000002.11:175622317:C:C 251375/251376, NC_000002.11:175622317:C:A 1/251376)
Row 2186985 (NC_000002.11:175622317:C:C 251362/251376, NC_000002.11:175622317:C:T 14/251376)

- Jul 13, 2019 (153)
24 GO Exome Sequencing Project NC_000002.11 - 175622318 Oct 11, 2018 (152)
25 KOREAN population from KRGDB NC_000002.11 - 175622318 Apr 25, 2020 (154)
26 Medical Genome Project healthy controls from Spanish population NC_000002.11 - 175622318 Apr 25, 2020 (154)
27 TopMed

Submission ignored due to conflicting rows:
Row 338338040 (NC_000002.12:174757589:C:A 2/264690)
Row 338338041 (NC_000002.12:174757589:C:T 30/264690)

- Apr 26, 2021 (155)
28 TopMed

Submission ignored due to conflicting rows:
Row 338338040 (NC_000002.12:174757589:C:A 2/264690)
Row 338338041 (NC_000002.12:174757589:C:T 30/264690)

- Apr 26, 2021 (155)
29 UK 10K study - Twins NC_000002.11 - 175622318 Oct 11, 2018 (152)
30 A Vietnamese Genetic Variation Database NC_000002.11 - 175622318 Jul 13, 2019 (153)
31 ALFA NC_000002.12 - 174757590 Apr 26, 2021 (155)
32 ClinVar RCV000387156.3 Oct 12, 2022 (156)
33 ClinVar RCV000642108.6 Oct 12, 2022 (156)
34 ClinVar RCV001313199.4 Oct 12, 2022 (156)
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
ss2733126796 NC_000002.11:175622317:C:A NC_000002.12:174757589:C:A (self)
RCV000387156.3, RCV001313199.4, 12658057580, ss2136848028, ss4534515161 NC_000002.12:174757589:C:A NC_000002.12:174757589:C:A (self)
12658057580 NC_000002.12:174757589:C:G NC_000002.12:174757589:C:G (self)
6393243, 6498689, 286537, 6842834, 104358, 6393243, 1390834, ss712467400, ss1605196572, ss1648190605, ss1686604540, ss1710987819, ss2733126796, ss2746820148, ss2783073798, ss3823828105, ss3899665440, ss5956629141 NC_000002.11:175622317:C:T NC_000002.12:174757589:C:T (self)
RCV000642108.6, 82528521, 12658057580, ss2236762244, ss3705471914, ss3802107551, ss4534515162, ss5450761542 NC_000002.12:174757589:C:T NC_000002.12:174757589: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 rs376844505

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.post761+d5e8e07