Name: rs34418780
Published: September 21, 2022
License: Open Access

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.

rs34418780

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:38893055 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.043613 (11544/264690, TOPMED)
T=0.048777 (6836/140148, GnomAD)
T=0.00177 (50/28258, 14KJPN) (+ 16 more)
T=0.05897 (1126/19096, ALFA)
T=0.00179 (30/16760, 8.3KJPN)
T=0.0314 (201/6404, 1000G_30x)
T=0.0302 (151/5008, 1000G)
T=0.0871 (390/4480, Estonian)
T=0.0641 (247/3854, ALSPAC)
T=0.0645 (239/3708, TWINSUK)
T=0.0034 (10/2922, KOREAN)
T=0.0071 (13/1832, Korea1K)
T=0.068 (68/998, GoNL)
T=0.127 (76/600, NorthernSweden)
T=0.009 (2/216, Qatari)
A=0.48 (20/42, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
A=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SCN11A : Intron 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	19096	A=0.94103	T=0.05897
European	Sub	14422	A=0.92934	T=0.07066
African	Sub	2976	A=0.9899	T=0.0101
African Others	Sub	114	A=1.000	T=0.000
African American	Sub	2862	A=0.9895	T=0.0105
Asian	Sub	114	A=1.000	T=0.000
East Asian	Sub	88	A=1.00	T=0.00
Other Asian	Sub	26	A=1.00	T=0.00
Latin American 1	Sub	150	A=0.973	T=0.027
Latin American 2	Sub	626	A=0.938	T=0.062
South Asian	Sub	98	A=0.94	T=0.06
Other	Sub	710	A=0.961	T=0.039

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.956387	T=0.043613
gnomAD - Genomes	Global	Study-wide	140148	A=0.951223	T=0.048777
gnomAD - Genomes	European	Sub	75846	A=0.93057	T=0.06943
gnomAD - Genomes	African	Sub	42048	A=0.98730	T=0.01270
gnomAD - Genomes	American	Sub	13650	A=0.93531	T=0.06469
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.9807	T=0.0193
gnomAD - Genomes	East Asian	Sub	3134	A=0.9984	T=0.0016
gnomAD - Genomes	Other	Sub	2150	A=0.9609	T=0.0391
14KJPN	JAPANESE	Study-wide	28258	A=0.99823	T=0.00177
Allele Frequency Aggregator	Total	Global	19096	A=0.94103	T=0.05897
Allele Frequency Aggregator	European	Sub	14422	A=0.92934	T=0.07066
Allele Frequency Aggregator	African	Sub	2976	A=0.9899	T=0.0101
Allele Frequency Aggregator	Other	Sub	710	A=0.961	T=0.039
Allele Frequency Aggregator	Latin American 2	Sub	626	A=0.938	T=0.062
Allele Frequency Aggregator	Latin American 1	Sub	150	A=0.973	T=0.027
Allele Frequency Aggregator	Asian	Sub	114	A=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=0.94	T=0.06
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99821	T=0.00179
1000Genomes_30x	Global	Study-wide	6404	A=0.9686	T=0.0314
1000Genomes_30x	African	Sub	1786	A=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	A=0.9423	T=0.0577
1000Genomes_30x	South Asian	Sub	1202	A=0.9401	T=0.0599
1000Genomes_30x	East Asian	Sub	1170	A=0.9966	T=0.0034
1000Genomes_30x	American	Sub	980	A=0.949	T=0.051
1000Genomes	Global	Study-wide	5008	A=0.9698	T=0.0302
1000Genomes	African	Sub	1322	A=0.9985	T=0.0015
1000Genomes	East Asian	Sub	1008	A=0.9970	T=0.0030
1000Genomes	Europe	Sub	1006	A=0.9463	T=0.0537
1000Genomes	South Asian	Sub	978	A=0.942	T=0.058
1000Genomes	American	Sub	694	A=0.950	T=0.050
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9129	T=0.0871
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9359	T=0.0641
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9355	T=0.0645
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9966	T=0.0034
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9929	T=0.0071
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.932	T=0.068
Northern Sweden	ACPOP	Study-wide	600	A=0.873	T=0.127
Qatari	Global	Study-wide	216	A=0.991	T=0.009
SGDP_PRJ	Global	Study-wide	42	A=0.48	T=0.52
The Danish reference pan genome	Danish	Study-wide	40	A=0.93	T=0.07
Siberian	Global	Study-wide	2	A=0.5	T=0.5

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.38893055A>T
GRCh37.p13 chr 3	NC_000003.11:g.38934546A>T
SCN11A RefSeqGene	NG_033859.2:g.163932T>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.2835+147… NM_001349253.2:c.2835+1478T>A	N/A	Intron Variant
SCN11A transcript variant 1	NM_014139.3:c.2835+1478T>A	N/A	Intron Variant
SCN11A transcript variant 3	NR_164473.1:n.	N/A	Genic Downstream Transcript Variant
SCN11A transcript variant X4	XM_011533321.3:c.2172+147… XM_011533321.3:c.2172+1478T>A	N/A	Intron Variant
SCN11A transcript variant X2	XM_017005650.2:c.2835+147… XM_017005650.2:c.2835+1478T>A	N/A	Intron Variant
SCN11A transcript variant X3	XM_017005651.2:c.2562+147… XM_017005651.2:c.2562+1478T>A	N/A	Intron Variant
SCN11A transcript variant X5	XM_017005653.2:c.1239+147… XM_017005653.2:c.1239+1478T>A	N/A	Intron Variant
SCN11A transcript variant X1	XM_047447378.1:c.3210+147… XM_047447378.1:c.3210+1478T>A	N/A	Intron Variant

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

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=	T
GRCh38.p14 chr 3	NC_000003.12:g.38893055=	NC_000003.12:g.38893055A>T
GRCh37.p13 chr 3	NC_000003.11:g.38934546=	NC_000003.11:g.38934546A>T
SCN11A RefSeqGene	NG_033859.2:g.163932=	NG_033859.2:g.163932T>A
SCN11A transcript variant 2	NM_001349253.2:c.2835+1478=	NM_001349253.2:c.2835+1478T>A
SCN11A transcript variant 1	NM_014139.2:c.2835+1478=	NM_014139.2:c.2835+1478T>A
SCN11A transcript variant 1	NM_014139.3:c.2835+1478=	NM_014139.3:c.2835+1478T>A
SCN11A transcript variant X1	XM_005264842.1:c.2835+1478=	XM_005264842.1:c.2835+1478T>A
SCN11A transcript variant X4	XM_011533321.3:c.2172+1478=	XM_011533321.3:c.2172+1478T>A
SCN11A transcript variant X2	XM_017005650.2:c.2835+1478=	XM_017005650.2:c.2835+1478T>A
SCN11A transcript variant X3	XM_017005651.2:c.2562+1478=	XM_017005651.2:c.2562+1478T>A
SCN11A transcript variant X5	XM_017005653.2:c.1239+1478=	XM_017005653.2:c.1239+1478T>A
SCN11A transcript variant X1	XM_047447378.1:c.3210+1478=	XM_047447378.1:c.3210+1478T>A

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#.

52 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41941052	Mar 13, 2006 (126)
2	HUMANGENOME_JCVI	ss96002520	Feb 04, 2009 (130)
3	1000GENOMES	ss231789532	Jul 14, 2010 (132)
4	ILLUMINA	ss483957146	May 04, 2012 (137)
5	ILLUMINA	ss484581973	May 04, 2012 (137)
6	ILLUMINA	ss536150977	Sep 08, 2015 (146)
7	ILLUMINA	ss780472154	Aug 21, 2014 (142)
8	ILLUMINA	ss782422567	Aug 21, 2014 (142)
9	ILLUMINA	ss835962497	Aug 21, 2014 (142)
10	EVA-GONL	ss978493744	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1070340300	Aug 21, 2014 (142)
12	1000GENOMES	ss1303619052	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1579928873	Apr 01, 2015 (144)
14	EVA_DECODE	ss1587962711	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1606861213	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1649855246	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1921738210	Feb 12, 2016 (147)
18	JJLAB	ss2021429523	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2149497693	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2250761917	Dec 20, 2016 (150)
21	ILLUMINA	ss2633938526	Nov 08, 2017 (151)
22	GNOMAD	ss2791837575	Nov 08, 2017 (151)
23	AFFY	ss2985875520	Nov 08, 2017 (151)
24	SWEGEN	ss2992157348	Nov 08, 2017 (151)
25	CSHL	ss3344979379	Nov 08, 2017 (151)
26	ILLUMINA	ss3628637438	Oct 12, 2018 (152)
27	ILLUMINA	ss3631885263	Oct 12, 2018 (152)
28	ILLUMINA	ss3642246577	Oct 12, 2018 (152)
29	URBANLAB	ss3647383318	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3660075577	Jul 13, 2019 (153)
31	EVA_DECODE	ss3709043029	Jul 13, 2019 (153)
32	ACPOP	ss3729809243	Jul 13, 2019 (153)
33	EVA	ss3759914984	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3803060940	Jul 13, 2019 (153)
35	EVA	ss3827764479	Apr 25, 2020 (154)
36	SGDP_PRJ	ss3855652838	Apr 25, 2020 (154)
37	KRGDB	ss3901466197	Apr 25, 2020 (154)
38	KOGIC	ss3951055529	Apr 25, 2020 (154)
39	TOPMED	ss4561265939	Apr 27, 2021 (155)
40	TOMMO_GENOMICS	ss5158710291	Apr 27, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5253754534	Oct 13, 2022 (156)
42	EVA	ss5314849975	Oct 13, 2022 (156)
43	EVA	ss5339190866	Oct 13, 2022 (156)
44	HUGCELL_USP	ss5453182927	Oct 13, 2022 (156)
45	EVA	ss5506960000	Oct 13, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5531950261	Oct 13, 2022 (156)
47	SANFORD_IMAGENETICS	ss5631951578	Oct 13, 2022 (156)
48	TOMMO_GENOMICS	ss5690233091	Oct 13, 2022 (156)
49	YY_MCH	ss5803659065	Oct 13, 2022 (156)
50	EVA	ss5825625007	Oct 13, 2022 (156)
51	EVA	ss5868449405	Oct 13, 2022 (156)
52	EVA	ss5960232503	Oct 13, 2022 (156)
53	1000Genomes	NC_000003.11 - 38934546	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000003.12 - 38893055	Oct 13, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 38934546	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000003.11 - 38934546	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000003.11 - 38934546	Apr 25, 2020 (154)
58	gnomAD - Genomes	NC_000003.12 - 38893055	Apr 27, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000003.11 - 38934546	Apr 25, 2020 (154)
60	KOREAN population from KRGDB	NC_000003.11 - 38934546	Apr 25, 2020 (154)
61	Korean Genome Project	NC_000003.12 - 38893055	Apr 25, 2020 (154)
62	Northern Sweden	NC_000003.11 - 38934546	Jul 13, 2019 (153)
63	Qatari	NC_000003.11 - 38934546	Apr 25, 2020 (154)
64	SGDP_PRJ	NC_000003.11 - 38934546	Apr 25, 2020 (154)
65	Siberian	NC_000003.11 - 38934546	Apr 25, 2020 (154)
66	8.3KJPN	NC_000003.11 - 38934546	Apr 27, 2021 (155)
67	14KJPN	NC_000003.12 - 38893055	Oct 13, 2022 (156)
68	TopMed	NC_000003.12 - 38893055	Apr 27, 2021 (155)
69	UK 10K study - Twins	NC_000003.11 - 38934546	Oct 12, 2018 (152)
70	ALFA	NC_000003.12 - 38893055	Apr 27, 2021 (155)

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
ss484581973, ss1587962711	NC_000003.10:38909549:A:T	NC_000003.12:38893054:A:T	(self)
14793546, 8220612, 5813825, 6093812, 3611668, 8643591, 3094108, 3780140, 7669818, 2014047, 16679598, 8220612, ss231789532, ss483957146, ss536150977, ss780472154, ss782422567, ss835962497, ss978493744, ss1070340300, ss1303619052, ss1579928873, ss1606861213, ss1649855246, ss1921738210, ss2021429523, ss2149497693, ss2633938526, ss2791837575, ss2985875520, ss2992157348, ss3344979379, ss3628637438, ss3631885263, ss3642246577, ss3660075577, ss3729809243, ss3759914984, ss3827764479, ss3855652838, ss3901466197, ss5158710291, ss5314849975, ss5339190866, ss5506960000, ss5631951578, ss5825625007, ss5960232503	NC_000003.11:38934545:A:T	NC_000003.12:38893054:A:T	(self)
19476196, 104927220, 7433530, 24070195, 398643494, 15418134925, ss2250761917, ss3647383318, ss3709043029, ss3803060940, ss3951055529, ss4561265939, ss5253754534, ss5453182927, ss5531950261, ss5690233091, ss5803659065, ss5868449405	NC_000003.12:38893054:A:T	NC_000003.12:38893054:A:T	(self)
ss41941052, ss96002520	NT_022517.18:38874545:A:T	NC_000003.12:38893054:A:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs34418780

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs34418780