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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.

rs199550149

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:166199716 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000416 (110/264690, TOPMED)
G=0.000322 (81/251484, GnomAD_exome)
G=0.000414 (58/140210, GnomAD) (+ 5 more)
G=0.000329 (40/121410, ExAC)
G=0.00060 (27/44788, ALFA)
G=0.00038 (5/13002, GO-ESP)
G=0.0005 (3/6404, 1000G_30x)
G=0.0004 (2/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SCN9A : Synonymous Variant
SCN1A-AS1 : Non Coding Transcript 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 44788 A=0.99940 G=0.00060
European Sub 32782 A=0.99930 G=0.00070
African Sub 3560 A=0.9997 G=0.0003
African Others Sub 122 A=1.000 G=0.000
African American Sub 3438 A=0.9997 G=0.0003
Asian Sub 168 A=1.000 G=0.000
East Asian Sub 112 A=1.000 G=0.000
Other Asian Sub 56 A=1.00 G=0.00
Latin American 1 Sub 500 A=1.000 G=0.000
Latin American 2 Sub 628 A=0.998 G=0.002
South Asian Sub 98 A=1.00 G=0.00
Other Sub 7052 A=0.9997 G=0.0003


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 A=0.999584 G=0.000416
gnomAD - Exomes Global Study-wide 251484 A=0.999678 G=0.000322
gnomAD - Exomes European Sub 135412 A=0.999454 G=0.000546
gnomAD - Exomes Asian Sub 49010 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34592 A=0.99988 G=0.00012
gnomAD - Exomes African Sub 16256 A=0.99988 G=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6134 A=0.9998 G=0.0002
gnomAD - Genomes Global Study-wide 140210 A=0.999586 G=0.000414
gnomAD - Genomes European Sub 75944 A=0.99945 G=0.00055
gnomAD - Genomes African Sub 42010 A=0.99971 G=0.00029
gnomAD - Genomes American Sub 13648 A=0.99993 G=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9986 G=0.0014
ExAC Global Study-wide 121410 A=0.999671 G=0.000329
ExAC Europe Sub 73354 A=0.99948 G=0.00052
ExAC Asian Sub 25164 A=1.00000 G=0.00000
ExAC American Sub 11578 A=0.99983 G=0.00017
ExAC African Sub 10406 A=1.00000 G=0.00000
ExAC Other Sub 908 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 44788 A=0.99940 G=0.00060
Allele Frequency Aggregator European Sub 32782 A=0.99930 G=0.00070
Allele Frequency Aggregator Other Sub 7052 A=0.9997 G=0.0003
Allele Frequency Aggregator African Sub 3560 A=0.9997 G=0.0003
Allele Frequency Aggregator Latin American 2 Sub 628 A=0.998 G=0.002
Allele Frequency Aggregator Latin American 1 Sub 500 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 168 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13002 A=0.99962 G=0.00038
GO Exome Sequencing Project European American Sub 8596 A=0.9994 G=0.0006
GO Exome Sequencing Project African American Sub 4406 A=1.0000 G=0.0000
1000Genomes_30x Global Study-wide 6404 A=0.9995 G=0.0005
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.998 G=0.002
1000Genomes Global Study-wide 5008 A=0.9996 G=0.0004
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9990 G=0.0010
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.999 G=0.001
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.166199716A>C
GRCh38.p14 chr 2 NC_000002.12:g.166199716A>G
GRCh37.p13 chr 2 NC_000002.11:g.167056226A>C
GRCh37.p13 chr 2 NC_000002.11:g.167056226A>G
SCN9A RefSeqGene (LRG_369) NG_012798.1:g.181272T>G
SCN9A RefSeqGene (LRG_369) NG_012798.1:g.181272T>C
Gene: SCN9A, sodium voltage-gated channel alpha subunit 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCN9A transcript variant 1 NM_002977.3:c.4890T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform 1 NP_002968.1:p.Leu1630= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant 1 NM_002977.3:c.4890T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform 1 NP_002968.1:p.Leu1630= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant 2 NM_001365536.1:c.4923T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform 2 NP_001352465.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant 2 NM_001365536.1:c.4923T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform 2 NP_001352465.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X5 XM_011511619.3:c.*137= N/A 3 Prime UTR Variant
SCN9A transcript variant X1 XM_011511617.3:c.4923T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X1 XP_011509919.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X1 XM_011511617.3:c.4923T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X1 XP_011509919.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X2 XM_011511616.4:c.4923T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X2 XP_011509918.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X2 XM_011511616.4:c.4923T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X2 XP_011509918.1:p.Leu1641= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X3 XM_011511618.3:c.4890T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X3 XP_011509920.1:p.Leu1630= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X3 XM_011511618.3:c.4890T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X3 XP_011509920.1:p.Leu1630= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X4 XM_017004669.2:c.4179T>G L [CTT] > L [CTG] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X4 XP_016860158.1:p.Leu1393= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X4 XM_017004669.2:c.4179T>C L [CTT] > L [CTC] Coding Sequence Variant
sodium channel protein type 9 subunit alpha isoform X4 XP_016860158.1:p.Leu1393= L (Leu) > L (Leu) Synonymous Variant
SCN9A transcript variant X6 XR_001738886.2:n. N/A Genic Downstream Transcript Variant
Gene: SCN1A-AS1, SCN1A and SCN9A antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SCN1A-AS1 transcript NR_110260.1:n.509A>C N/A Non Coding Transcript Variant
SCN1A-AS1 transcript NR_110260.1:n.509A>G 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: C (allele ID: 1132374 )
ClinVar Accession Disease Names Clinical Significance
RCV001494831.4 Generalized epilepsy with febrile seizures plus, type 7,Neuropathy, hereditary sensory and autonomic, type 2A Likely-Benign
Allele: G (allele ID: 135719 )
ClinVar Accession Disease Names Clinical Significance
RCV000118310.9 not specified Benign
RCV000240565.17 not provided Likely-Benign
RCV001086623.6 Generalized epilepsy with febrile seizures plus, type 7,Neuropathy, hereditary sensory and autonomic, type 2A Likely-Benign
RCV001131479.3 Channelopathy-associated congenital insensitivity to pain, autosomal recessive Uncertain-Significance
RCV001131480.3 Primary erythromelalgia Benign
RCV001131481.3 Paroxysmal extreme pain disorder Benign
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 A= C G
GRCh38.p14 chr 2 NC_000002.12:g.166199716= NC_000002.12:g.166199716A>C NC_000002.12:g.166199716A>G
GRCh37.p13 chr 2 NC_000002.11:g.167056226= NC_000002.11:g.167056226A>C NC_000002.11:g.167056226A>G
SCN9A RefSeqGene (LRG_369) NG_012798.1:g.181272= NG_012798.1:g.181272T>G NG_012798.1:g.181272T>C
SCN9A transcript variant 1 NM_002977.3:c.4890= NM_002977.3:c.4890T>G NM_002977.3:c.4890T>C
SCN9A transcript variant 2 NM_001365536.1:c.4923= NM_001365536.1:c.4923T>G NM_001365536.1:c.4923T>C
SCN9A transcript variant X2 XM_011511616.4:c.4923= XM_011511616.4:c.4923T>G XM_011511616.4:c.4923T>C
SCN9A transcript variant X2 XM_011511616.3:c.4923= XM_011511616.3:c.4923T>G XM_011511616.3:c.4923T>C
SCN9A transcript variant X2 XM_011511616.2:c.4923= XM_011511616.2:c.4923T>G XM_011511616.2:c.4923T>C
SCN9A transcript variant X2 XM_011511616.1:c.4923= XM_011511616.1:c.4923T>G XM_011511616.1:c.4923T>C
SCN9A transcript variant X1 XM_011511617.3:c.4923= XM_011511617.3:c.4923T>G XM_011511617.3:c.4923T>C
SCN9A transcript variant X3 XM_011511617.2:c.4923= XM_011511617.2:c.4923T>G XM_011511617.2:c.4923T>C
SCN9A transcript variant X3 XM_011511617.1:c.4923= XM_011511617.1:c.4923T>G XM_011511617.1:c.4923T>C
SCN9A transcript variant X3 XM_011511618.3:c.4890= XM_011511618.3:c.4890T>G XM_011511618.3:c.4890T>C
SCN9A transcript variant X4 XM_011511618.2:c.4890= XM_011511618.2:c.4890T>G XM_011511618.2:c.4890T>C
SCN9A transcript variant X4 XM_011511618.1:c.4890= XM_011511618.1:c.4890T>G XM_011511618.1:c.4890T>C
SCN9A transcript variant X5 XM_011511619.3:c.*137= XM_011511619.3:c.*137T>G XM_011511619.3:c.*137T>C
SCN9A transcript variant X4 XM_017004669.2:c.4179= XM_017004669.2:c.4179T>G XM_017004669.2:c.4179T>C
SCN9A transcript variant X6 XM_017004669.1:c.4179= XM_017004669.1:c.4179T>G XM_017004669.1:c.4179T>C
SCN1A-AS1 transcript NR_110260.1:n.509= NR_110260.1:n.509A>C NR_110260.1:n.509A>G
sodium channel protein type 9 subunit alpha isoform 1 NP_002968.1:p.Leu1630= NP_002968.1:p.Leu1630= NP_002968.1:p.Leu1630=
sodium channel protein type 9 subunit alpha isoform 2 NP_001352465.1:p.Leu1641= NP_001352465.1:p.Leu1641= NP_001352465.1:p.Leu1641=
sodium channel protein type 9 subunit alpha isoform X2 XP_011509918.1:p.Leu1641= XP_011509918.1:p.Leu1641= XP_011509918.1:p.Leu1641=
sodium channel protein type 9 subunit alpha isoform X1 XP_011509919.1:p.Leu1641= XP_011509919.1:p.Leu1641= XP_011509919.1:p.Leu1641=
sodium channel protein type 9 subunit alpha isoform X3 XP_011509920.1:p.Leu1630= XP_011509920.1:p.Leu1630= XP_011509920.1:p.Leu1630=
sodium channel protein type 9 subunit alpha isoform X4 XP_016860158.1:p.Leu1393= XP_016860158.1:p.Leu1393= XP_016860158.1:p.Leu1393=
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#.

19 SubSNP, 8 Frequency, 7 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488730259 May 04, 2012 (137)
2 GSK-GENETICS ss491259690 May 04, 2012 (137)
3 CLINSEQ_SNP ss491793862 May 04, 2012 (137)
4 NHLBI-ESP ss712463165 Apr 25, 2013 (138)
5 1000GENOMES ss1300280300 Aug 21, 2014 (142)
6 CLINVAR ss1457615285 Nov 23, 2014 (142)
7 EVA_EXAC ss1686576049 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2236274441 Dec 20, 2016 (150)
9 GNOMAD ss2733081580 Nov 08, 2017 (151)
10 GNOMAD ss2746807119 Nov 08, 2017 (151)
11 GNOMAD ss2782398659 Nov 08, 2017 (151)
12 SWEGEN ss2990804414 Nov 08, 2017 (151)
13 EVA ss3823822156 Apr 25, 2020 (154)
14 TOPMED ss4532467614 Apr 26, 2021 (155)
15 1000G_HIGH_COVERAGE ss5250839175 Oct 12, 2022 (156)
16 EVA ss5333864247 Oct 12, 2022 (156)
17 1000G_HIGH_COVERAGE ss5527560951 Oct 12, 2022 (156)
18 EVA ss5821126543 Oct 12, 2022 (156)
19 EVA ss5933331329 Oct 12, 2022 (156)
20 1000Genomes NC_000002.11 - 167056226 Oct 11, 2018 (152)
21 1000Genomes_30x NC_000002.12 - 166199716 Oct 12, 2022 (156)
22 ExAC NC_000002.11 - 167056226 Oct 11, 2018 (152)
23 gnomAD - Genomes NC_000002.12 - 166199716 Apr 26, 2021 (155)
24 gnomAD - Exomes NC_000002.11 - 167056226 Jul 13, 2019 (153)
25 GO Exome Sequencing Project NC_000002.11 - 167056226 Oct 11, 2018 (152)
26 TopMed NC_000002.12 - 166199716 Apr 26, 2021 (155)
27 ALFA NC_000002.12 - 166199716 Apr 26, 2021 (155)
28 ClinVar RCV000118310.9 Oct 12, 2022 (156)
29 ClinVar RCV000240565.17 Oct 12, 2022 (156)
30 ClinVar RCV001086623.6 Oct 12, 2022 (156)
31 ClinVar RCV001131479.3 Oct 12, 2022 (156)
32 ClinVar RCV001131480.3 Oct 12, 2022 (156)
33 ClinVar RCV001131481.3 Oct 12, 2022 (156)
34 ClinVar RCV001494831.4 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
RCV001494831.4 NC_000002.12:166199715:A:C NC_000002.12:166199715:A:C
ss491259690, ss491793862 NC_000002.10:166764471:A:G NC_000002.12:166199715:A:G (self)
11331918, 6467694, 2140389, 280590, ss488730259, ss712463165, ss1300280300, ss1686576049, ss2733081580, ss2746807119, ss2782398659, ss2990804414, ss3823822156, ss5333864247, ss5821126543 NC_000002.11:167056225:A:G NC_000002.12:166199715:A:G (self)
RCV000118310.9, RCV000240565.17, RCV001086623.6, RCV001131479.3, RCV001131480.3, RCV001131481.3, 15086886, 80802688, 336290493, 5597434154, ss1457615285, ss2236274441, ss4532467614, ss5250839175, ss5527560951, ss5933331329 NC_000002.12:166199715:A:G NC_000002.12:166199715:A:G (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 rs199550149

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