Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs78953918

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:38850578 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.003710 (982/264690, TOPMED)
T=0.006129 (1539/251082, GnomAD_exome)
T=0.004796 (672/140110, GnomAD) (+ 17 more)
T=0.005643 (685/121380, ExAC)
T=0.00663 (329/49632, ALFA)
T=0.00004 (1/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00492 (64/13006, GO-ESP)
T=0.0025 (16/6404, 1000G_30x)
T=0.0026 (13/5008, 1000G)
T=0.0103 (46/4480, Estonian)
T=0.0057 (22/3854, ALSPAC)
T=0.0049 (18/3708, TWINSUK)
T=0.009 (9/998, GoNL)
T=0.007 (4/600, NorthernSweden)
T=0.004 (2/534, MGP)
T=0.003 (1/304, FINRISK)
T=0.009 (2/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SCN11A : Synonymous 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 65922 C=0.99370 T=0.00630
European Sub 47316 C=0.99258 T=0.00742
African Sub 8432 C=0.9987 T=0.0013
African Others Sub 306 C=1.000 T=0.000
African American Sub 8126 C=0.9986 T=0.0014
Asian Sub 172 C=1.000 T=0.000
East Asian Sub 114 C=1.000 T=0.000
Other Asian Sub 58 C=1.00 T=0.00
Latin American 1 Sub 508 C=1.000 T=0.000
Latin American 2 Sub 634 C=0.995 T=0.005
South Asian Sub 98 C=1.00 T=0.00
Other Sub 8762 C=0.9943 T=0.0057


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 C=0.996290 T=0.003710
gnomAD - Exomes Global Study-wide 251082 C=0.993871 T=0.006129
gnomAD - Exomes European Sub 135052 C=0.992218 T=0.007782
gnomAD - Exomes Asian Sub 48998 C=0.99680 T=0.00320
gnomAD - Exomes American Sub 34588 C=0.99691 T=0.00309
gnomAD - Exomes African Sub 16252 C=0.99883 T=0.00117
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=0.98391 T=0.01609
gnomAD - Exomes Other Sub 6124 C=0.9930 T=0.0070
gnomAD - Genomes Global Study-wide 140110 C=0.995204 T=0.004796
gnomAD - Genomes European Sub 75892 C=0.99321 T=0.00679
gnomAD - Genomes African Sub 41978 C=0.99890 T=0.00110
gnomAD - Genomes American Sub 13642 C=0.99648 T=0.00352
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9841 T=0.0159
gnomAD - Genomes East Asian Sub 3124 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9953 T=0.0047
ExAC Global Study-wide 121380 C=0.994357 T=0.005643
ExAC Europe Sub 73340 C=0.99260 T=0.00740
ExAC Asian Sub 25154 C=0.99650 T=0.00350
ExAC American Sub 11572 C=0.99715 T=0.00285
ExAC African Sub 10406 C=0.99933 T=0.00067
ExAC Other Sub 908 C=0.985 T=0.015
Allele Frequency Aggregator Total Global 49632 C=0.99337 T=0.00663
Allele Frequency Aggregator European Sub 37294 C=0.99255 T=0.00745
Allele Frequency Aggregator Other Sub 7328 C=0.9943 T=0.0057
Allele Frequency Aggregator African Sub 3598 C=0.9983 T=0.0017
Allele Frequency Aggregator Latin American 2 Sub 634 C=0.995 T=0.005
Allele Frequency Aggregator Latin American 1 Sub 508 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 172 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
14KJPN JAPANESE Study-wide 28258 C=0.99996 T=0.00004
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
GO Exome Sequencing Project Global Study-wide 13006 C=0.99508 T=0.00492
GO Exome Sequencing Project European American Sub 8600 C=0.9931 T=0.0069
GO Exome Sequencing Project African American Sub 4406 C=0.9989 T=0.0011
1000Genomes_30x Global Study-wide 6404 C=0.9975 T=0.0025
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9913 T=0.0087
1000Genomes_30x South Asian Sub 1202 C=0.9992 T=0.0008
1000Genomes_30x East Asian Sub 1170 C=0.9991 T=0.0009
1000Genomes_30x American Sub 980 C=0.997 T=0.003
1000Genomes Global Study-wide 5008 C=0.9974 T=0.0026
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9990 T=0.0010
1000Genomes Europe Sub 1006 C=0.9911 T=0.0089
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=0.997 T=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9897 T=0.0103
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9943 T=0.0057
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9951 T=0.0049
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.991 T=0.009
Northern Sweden ACPOP Study-wide 600 C=0.993 T=0.007
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 T=0.004
FINRISK Finnish from FINRISK project Study-wide 304 C=0.997 T=0.003
Qatari Global Study-wide 216 C=0.991 T=0.009
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
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 3 NC_000003.12:g.38850578C>T
GRCh37.p13 chr 3 NC_000003.11:g.38892069C>T
SCN11A RefSeqGene NG_033859.2:g.206409G>A
Gene: SCN11A, sodium voltage-gated channel alpha subunit 11 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCN11A transcript variant 2 NM_001349253.2:c.4230G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha NP_001336182.1:p.Thr1410= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant 1 NM_014139.3:c.4230G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha NP_054858.2:p.Thr1410= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant 3 NR_164473.1:n. N/A Genic Downstream Transcript Variant
SCN11A transcript variant X1 XM_047447378.1:c.4605G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha isoform X1 XP_047303334.1:p.Thr1535= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant X2 XM_017005650.2:c.4230G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha isoform X2 XP_016861139.1:p.Thr1410= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant X3 XM_017005651.2:c.3957G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha isoform X3 XP_016861140.1:p.Thr1319= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant X4 XM_011533321.3:c.3567G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha isoform X4 XP_011531623.1:p.Thr1189= T (Thr) > T (Thr) Synonymous Variant
SCN11A transcript variant X5 XM_017005653.2:c.2634G>A T [ACG] > T [ACA] Coding Sequence Variant
sodium channel protein type 11 subunit alpha isoform X5 XP_016861142.1:p.Thr878= T (Thr) > T (Thr) Synonymous 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: 452344 )
ClinVar Accession Disease Names Clinical Significance
RCV000541093.7 Familial episodic pain syndrome with predominantly lower limb involvement,Hereditary sensory and autonomic neuropathy type 7 Benign
RCV001584335.4 not provided Benign-Likely-Benign
RCV001701082.4 not specified 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 C= T
GRCh38.p14 chr 3 NC_000003.12:g.38850578= NC_000003.12:g.38850578C>T
GRCh37.p13 chr 3 NC_000003.11:g.38892069= NC_000003.11:g.38892069C>T
SCN11A RefSeqGene NG_033859.2:g.206409= NG_033859.2:g.206409G>A
SCN11A transcript variant 1 NM_014139.3:c.4230= NM_014139.3:c.4230G>A
SCN11A transcript variant 1 NM_014139.2:c.4230= NM_014139.2:c.4230G>A
SCN11A transcript variant 2 NM_001349253.2:c.4230= NM_001349253.2:c.4230G>A
SCN11A transcript variant 2 NM_001349253.1:c.4230= NM_001349253.1:c.4230G>A
SCN11A transcript variant X4 XM_011533321.3:c.3567= XM_011533321.3:c.3567G>A
SCN11A transcript variant X5 XM_011533321.2:c.3567= XM_011533321.2:c.3567G>A
SCN11A transcript variant X2 XM_011533321.1:c.3567= XM_011533321.1:c.3567G>A
SCN11A transcript variant X2 XM_017005650.2:c.4230= XM_017005650.2:c.4230G>A
SCN11A transcript variant X3 XM_017005650.1:c.4230= XM_017005650.1:c.4230G>A
SCN11A transcript variant X3 XM_017005651.2:c.3957= XM_017005651.2:c.3957G>A
SCN11A transcript variant X4 XM_017005651.1:c.3957= XM_017005651.1:c.3957G>A
SCN11A transcript variant X5 XM_017005653.2:c.2634= XM_017005653.2:c.2634G>A
SCN11A transcript variant X7 XM_017005653.1:c.2634= XM_017005653.1:c.2634G>A
SCN11A transcript variant X1 XM_047447378.1:c.4605= XM_047447378.1:c.4605G>A
SCN11A transcript variant 2 NM_001287223.1:c.4230= NM_001287223.1:c.4230G>A
sodium channel protein type 11 subunit alpha NP_054858.2:p.Thr1410= NP_054858.2:p.Thr1410=
sodium channel protein type 11 subunit alpha NP_001336182.1:p.Thr1410= NP_001336182.1:p.Thr1410=
sodium channel protein type 11 subunit alpha isoform X4 XP_011531623.1:p.Thr1189= XP_011531623.1:p.Thr1189=
sodium channel protein type 11 subunit alpha isoform X2 XP_016861139.1:p.Thr1410= XP_016861139.1:p.Thr1410=
sodium channel protein type 11 subunit alpha isoform X3 XP_016861140.1:p.Thr1319= XP_016861140.1:p.Thr1319=
sodium channel protein type 11 subunit alpha isoform X5 XP_016861142.1:p.Thr878= XP_016861142.1:p.Thr878=
sodium channel protein type 11 subunit alpha isoform X1 XP_047303334.1:p.Thr1535= XP_047303334.1:p.Thr1535=
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#.

40 SubSNP, 19 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss231789435 Jul 14, 2010 (132)
2 NHLBI-ESP ss342120803 May 09, 2011 (134)
3 1000GENOMES ss489871781 May 04, 2012 (137)
4 CLINSEQ_SNP ss491831673 May 04, 2012 (137)
5 ILLUMINA ss535859935 Sep 08, 2015 (146)
6 EVA-GONL ss978493474 Aug 21, 2014 (142)
7 1000GENOMES ss1303617993 Aug 21, 2014 (142)
8 EVA_FINRISK ss1584026776 Apr 01, 2015 (144)
9 EVA_DECODE ss1587962452 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1606860642 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1649854675 Apr 01, 2015 (144)
12 EVA_EXAC ss1686935777 Apr 01, 2015 (144)
13 EVA_MGP ss1711013089 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1921737922 Feb 12, 2016 (147)
15 JJLAB ss2021429392 Sep 14, 2016 (149)
16 HUMAN_LONGEVITY ss2250759748 Dec 20, 2016 (150)
17 GNOMAD ss2733643480 Nov 08, 2017 (151)
18 GNOMAD ss2746976496 Nov 08, 2017 (151)
19 GNOMAD ss2791834712 Nov 08, 2017 (151)
20 SWEGEN ss2992156983 Nov 08, 2017 (151)
21 CSHL ss3344979271 Nov 08, 2017 (151)
22 ILLUMINA ss3628637382 Oct 12, 2018 (152)
23 EGCUT_WGS ss3660075122 Jul 13, 2019 (153)
24 EVA_DECODE ss3709042603 Jul 13, 2019 (153)
25 ACPOP ss3729809034 Jul 13, 2019 (153)
26 EVA ss3759914651 Jul 13, 2019 (153)
27 EVA ss3823898397 Apr 25, 2020 (154)
28 SGDP_PRJ ss3855652336 Apr 25, 2020 (154)
29 EVA ss3986233582 Apr 27, 2021 (155)
30 TOPMED ss4561256802 Apr 27, 2021 (155)
31 TOMMO_GENOMICS ss5158709267 Apr 27, 2021 (155)
32 1000G_HIGH_COVERAGE ss5253753713 Oct 13, 2022 (156)
33 HUGCELL_USP ss5453182176 Oct 13, 2022 (156)
34 1000G_HIGH_COVERAGE ss5531949000 Oct 13, 2022 (156)
35 SANFORD_IMAGENETICS ss5631951125 Oct 13, 2022 (156)
36 TOMMO_GENOMICS ss5690231731 Oct 13, 2022 (156)
37 EVA ss5825624679 Oct 13, 2022 (156)
38 EVA ss5848579185 Oct 13, 2022 (156)
39 EVA ss5868448383 Oct 13, 2022 (156)
40 EVA ss5960231949 Oct 13, 2022 (156)
41 1000Genomes NC_000003.11 - 38892069 Oct 12, 2018 (152)
42 1000Genomes_30x NC_000003.12 - 38850578 Oct 13, 2022 (156)
43 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 38892069 Oct 12, 2018 (152)
44 Genetic variation in the Estonian population NC_000003.11 - 38892069 Oct 12, 2018 (152)
45 ExAC NC_000003.11 - 38892069 Oct 12, 2018 (152)
46 FINRISK NC_000003.11 - 38892069 Apr 25, 2020 (154)
47 gnomAD - Genomes NC_000003.12 - 38850578 Apr 27, 2021 (155)
48 gnomAD - Exomes NC_000003.11 - 38892069 Jul 13, 2019 (153)
49 GO Exome Sequencing Project NC_000003.11 - 38892069 Oct 12, 2018 (152)
50 Genome of the Netherlands Release 5 NC_000003.11 - 38892069 Apr 25, 2020 (154)
51 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 38892069 Apr 25, 2020 (154)
52 Northern Sweden NC_000003.11 - 38892069 Jul 13, 2019 (153)
53 Qatari NC_000003.11 - 38892069 Apr 25, 2020 (154)
54 SGDP_PRJ NC_000003.11 - 38892069 Apr 25, 2020 (154)
55 8.3KJPN NC_000003.11 - 38892069 Apr 27, 2021 (155)
56 14KJPN NC_000003.12 - 38850578 Oct 13, 2022 (156)
57 TopMed NC_000003.12 - 38850578 Apr 27, 2021 (155)
58 UK 10K study - Twins NC_000003.11 - 38892069 Oct 12, 2018 (152)
59 ALFA NC_000003.12 - 38850578 Apr 27, 2021 (155)
60 ClinVar RCV000541093.7 Oct 13, 2022 (156)
61 ClinVar RCV001584335.4 Oct 13, 2022 (156)
62 ClinVar RCV001701082.4 Oct 13, 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
ss491831673, ss1587962452 NC_000003.10:38867072:C:T NC_000003.12:38850577:C:T (self)
14792457, 8219995, 5813370, 6855056, 23237, 2718583, 356748, 3611401, 129628, 3093899, 3779852, 7669316, 16678574, 8219995, ss231789435, ss342120803, ss489871781, ss535859935, ss978493474, ss1303617993, ss1584026776, ss1606860642, ss1649854675, ss1686935777, ss1711013089, ss1921737922, ss2021429392, ss2733643480, ss2746976496, ss2791834712, ss2992156983, ss3344979271, ss3628637382, ss3660075122, ss3729809034, ss3759914651, ss3823898397, ss3855652336, ss3986233582, ss5158709267, ss5631951125, ss5825624679, ss5848579185, ss5960231949 NC_000003.11:38892068:C:T NC_000003.12:38850577:C:T (self)
RCV000541093.7, RCV001584335.4, RCV001701082.4, 19474935, 104919836, 24068835, 398634357, 5009398227, ss2250759748, ss3709042603, ss4561256802, ss5253753713, ss5453182176, ss5531949000, ss5690231731, ss5868448383 NC_000003.12:38850577:C:T NC_000003.12:38850577: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 rs78953918

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