Name: rs35100587
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.

rs35100587

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:14139206 (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=0.020556 (5441/264690, TOPMED)
T=0.018442 (4637/251432, GnomAD_exome)
T=0.020121 (2822/140254, GnomAD) (+ 17 more)
T=0.019962 (2423/121382, ExAC)
T=0.01909 (1502/78686, PAGE_STUDY)
T=0.01940 (976/50302, ALFA)
T=0.02130 (277/13006, GO-ESP)
T=0.0228 (146/6404, 1000G_30x)
T=0.0214 (107/5008, 1000G)
T=0.0150 (67/4480, Estonian)
T=0.0223 (86/3854, ALSPAC)
T=0.0218 (81/3708, TWINSUK)
T=0.018 (18/998, GoNL)
T=0.012 (7/600, NorthernSweden)
T=0.021 (11/534, MGP)
T=0.013 (4/304, FINRISK)
T=0.009 (2/216, Qatari)
T=0.005 (1/216, Vietnamese)
C=0.50 (9/18, SGDP_PRJ)
T=0.50 (9/18, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: TMEM43 : Synonymous Variant
Publications: 2 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	66634	C=0.98006	T=0.01994
European	Sub	47374	C=0.98092	T=0.01908
African	Sub	8854	C=0.9721	T=0.0279
African Others	Sub	306	C=0.954	T=0.046
African American	Sub	8548	C=0.9727	T=0.0273
Asian	Sub	206	C=1.000	T=0.000
East Asian	Sub	148	C=1.000	T=0.000
Other Asian	Sub	58	C=1.00	T=0.00
Latin American 1	Sub	508	C=0.986	T=0.014
Latin American 2	Sub	634	C=0.987	T=0.013
South Asian	Sub	104	C=0.990	T=0.010
Other	Sub	8954	C=0.9819	T=0.0181

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	C=0.979444	T=0.020556
gnomAD - Exomes	Global	Study-wide	251432	C=0.981558	T=0.018442
gnomAD - Exomes	European	Sub	135372	C=0.980151	T=0.019849
gnomAD - Exomes	Asian	Sub	49008	C=0.98078	T=0.01922
gnomAD - Exomes	American	Sub	34584	C=0.98956	T=0.01044
gnomAD - Exomes	African	Sub	16252	C=0.97077	T=0.02923
gnomAD - Exomes	Ashkenazi Jewish	Sub	10080	C=0.99425	T=0.00575
gnomAD - Exomes	Other	Sub	6136	C=0.9814	T=0.0186
gnomAD - Genomes	Global	Study-wide	140254	C=0.979879	T=0.020121
gnomAD - Genomes	European	Sub	75944	C=0.98251	T=0.01749
gnomAD - Genomes	African	Sub	42038	C=0.97060	T=0.02940
gnomAD - Genomes	American	Sub	13662	C=0.98595	T=0.01405
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9931	T=0.0069
gnomAD - Genomes	East Asian	Sub	3134	C=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2152	C=0.9805	T=0.0195
ExAC	Global	Study-wide	121382	C=0.980038	T=0.019962
ExAC	Europe	Sub	73334	C=0.97986	T=0.02014
ExAC	Asian	Sub	25166	C=0.97922	T=0.02078
ExAC	American	Sub	11574	C=0.99076	T=0.00924
ExAC	African	Sub	10402	C=0.97116	T=0.02884
ExAC	Other	Sub	906	C=0.982	T=0.018
The PAGE Study	Global	Study-wide	78686	C=0.98091	T=0.01909
The PAGE Study	AfricanAmerican	Sub	32502	C=0.97252	T=0.02748
The PAGE Study	Mexican	Sub	10810	C=0.98788	T=0.01212
The PAGE Study	Asian	Sub	8318	C=0.9993	T=0.0007
The PAGE Study	PuertoRican	Sub	7918	C=0.9785	T=0.0215
The PAGE Study	NativeHawaiian	Sub	4532	C=0.9938	T=0.0062
The PAGE Study	Cuban	Sub	4230	C=0.9790	T=0.0210
The PAGE Study	Dominican	Sub	3828	C=0.9804	T=0.0196
The PAGE Study	CentralAmerican	Sub	2450	C=0.9820	T=0.0180
The PAGE Study	SouthAmerican	Sub	1982	C=0.9889	T=0.0111
The PAGE Study	NativeAmerican	Sub	1260	C=0.9841	T=0.0159
The PAGE Study	SouthAsian	Sub	856	C=0.972	T=0.028
Allele Frequency Aggregator	Total	Global	50302	C=0.98060	T=0.01940
Allele Frequency Aggregator	European	Sub	37312	C=0.98062	T=0.01938
Allele Frequency Aggregator	Other	Sub	7522	C=0.9823	T=0.0177
Allele Frequency Aggregator	African	Sub	4016	C=0.9741	T=0.0259
Allele Frequency Aggregator	Latin American 2	Sub	634	C=0.987	T=0.013
Allele Frequency Aggregator	Latin American 1	Sub	508	C=0.986	T=0.014
Allele Frequency Aggregator	Asian	Sub	206	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	104	C=0.990	T=0.010
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.97870	T=0.02130
GO Exome Sequencing Project	European American	Sub	8600	C=0.9800	T=0.0200
GO Exome Sequencing Project	African American	Sub	4406	C=0.9762	T=0.0238
1000Genomes_30x	Global	Study-wide	6404	C=0.9772	T=0.0228
1000Genomes_30x	African	Sub	1786	C=0.9653	T=0.0347
1000Genomes_30x	Europe	Sub	1266	C=0.9724	T=0.0276
1000Genomes_30x	South Asian	Sub	1202	C=0.9734	T=0.0266
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.983	T=0.017
1000Genomes	Global	Study-wide	5008	C=0.9786	T=0.0214
1000Genomes	African	Sub	1322	C=0.9637	T=0.0363
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9761	T=0.0239
1000Genomes	South Asian	Sub	978	C=0.975	T=0.025
1000Genomes	American	Sub	694	C=0.984	T=0.016
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9850	T=0.0150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9777	T=0.0223
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9782	T=0.0218
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.982	T=0.018
Northern Sweden	ACPOP	Study-wide	600	C=0.988	T=0.012
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.979	T=0.021
FINRISK	Finnish from FINRISK project	Study-wide	304	C=0.987	T=0.013
Qatari	Global	Study-wide	216	C=0.991	T=0.009
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	18	C=0.50	T=0.50

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.14139206C>T
GRCh37.p13 chr 3	NC_000003.11:g.14180706C>T
TMEM43 RefSeqGene (LRG_435)	NG_008975.1:g.19267C>T

Gene: TMEM43, transmembrane protein 43 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM43 transcript variant 1	NM_024334.3:c.909C>T	S [AGC] > S [AGT]	Coding Sequence Variant
transmembrane protein 43 isoform 1	NP_077310.1:p.Ser303=	S (Ser) > S (Ser)	Synonymous 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.

Allele: T (allele ID: 55319 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000039393.14	not specified	Benign
RCV000241757.2	Cardiovascular phenotype	Benign
RCV000477225.8	Arrhythmogenic right ventricular dysplasia 5	Benign
RCV000771074.2	Cardiomyopathy	Benign
RCV001650876.5	not provided	Benign

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.14139206=	NC_000003.12:g.14139206C>T
GRCh37.p13 chr 3	NC_000003.11:g.14180706=	NC_000003.11:g.14180706C>T
TMEM43 RefSeqGene (LRG_435)	NG_008975.1:g.19267=	NG_008975.1:g.19267C>T
TMEM43 transcript variant 1	NM_024334.3:c.909=	NM_024334.3:c.909C>T
TMEM43 transcript	NM_024334.2:c.909=	NM_024334.2:c.909C>T
TMEM43 transcript variant 2	NM_001407274.1:c.912=	NM_001407274.1:c.912C>T
TMEM43 transcript variant 4	NM_001407276.1:c.906=	NM_001407276.1:c.906C>T
TMEM43 transcript variant 3	NM_001407275.1:c.906=	NM_001407275.1:c.906C>T
TMEM43 transcript variant 5	NM_001407277.1:c.903=	NM_001407277.1:c.903C>T
TMEM43 transcript variant 6	NM_001407278.1:c.894=	NM_001407278.1:c.894C>T
TMEM43 transcript variant 7	NM_001407279.1:c.834=	NM_001407279.1:c.834C>T
TMEM43 transcript variant 8	NM_001407280.1:c.759=	NM_001407280.1:c.759C>T
transmembrane protein 43 isoform 1	NP_077310.1:p.Ser303=	NP_077310.1:p.Ser303=

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#.

60 SubSNP, 19 Frequency, 5 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	APPLERA_GI	ss48423852	Mar 14, 2006 (126)
2	COMPLETE_GENOMICS	ss161929092	Jul 04, 2010 (132)
3	1000GENOMES	ss211140004	Jul 14, 2010 (132)
4	1000GENOMES	ss219992319	Jul 14, 2010 (132)
5	NHLBI-ESP	ss342115326	May 09, 2011 (134)
6	1000GENOMES	ss489866466	May 04, 2012 (137)
7	CLINSEQ_SNP	ss491829619	May 04, 2012 (137)
8	ILLUMINA	ss536489191	Sep 08, 2015 (146)
9	JMKIDD_LAB	ss974447128	Aug 21, 2014 (142)
10	EVA-GONL	ss978294527	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1067448572	Aug 21, 2014 (142)
12	1000GENOMES	ss1302888771	Aug 21, 2014 (142)
13	DDI	ss1429337294	Apr 01, 2015 (144)
14	EVA_FINRISK	ss1584026038	Apr 01, 2015 (144)
15	EVA_DECODE	ss1587756367	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1606460808	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1649454841	Apr 01, 2015 (144)
18	EVA_EXAC	ss1686882167	Apr 01, 2015 (144)
19	EVA_MGP	ss1711008343	Apr 01, 2015 (144)
20	EVA_MCP	ss1815616621	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1921547361	Feb 12, 2016 (147)
22	ILLUMINA	ss1958539480	Feb 12, 2016 (147)
23	JJLAB	ss2021327184	Sep 14, 2016 (149)
24	HUMAN_LONGEVITY	ss2249248762	Dec 20, 2016 (150)
25	GNOMAD	ss2733561173	Nov 08, 2017 (151)
26	GNOMAD	ss2746952031	Nov 08, 2017 (151)
27	GNOMAD	ss2789772052	Nov 08, 2017 (151)
28	SWEGEN	ss2991864056	Nov 08, 2017 (151)
29	ILLUMINA	ss3022214099	Nov 08, 2017 (151)
30	ILLUMINA	ss3628595596	Oct 11, 2018 (152)
31	OMUKHERJEE_ADBS	ss3646283180	Oct 11, 2018 (152)
32	ILLUMINA	ss3652680328	Oct 11, 2018 (152)
33	EGCUT_WGS	ss3659764550	Jul 13, 2019 (153)
34	EVA_DECODE	ss3708679618	Jul 13, 2019 (153)
35	ILLUMINA	ss3725992334	Jul 13, 2019 (153)
36	ACPOP	ss3729650482	Jul 13, 2019 (153)
37	PAGE_CC	ss3771012473	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3802837005	Jul 13, 2019 (153)
39	EVA	ss3823886832	Apr 25, 2020 (154)
40	EVA	ss3825627102	Apr 25, 2020 (154)
41	EVA	ss3827672212	Apr 25, 2020 (154)
42	EVA	ss3836377991	Apr 25, 2020 (154)
43	SGDP_PRJ	ss3855272266	Apr 25, 2020 (154)
44	FSA-LAB	ss3984243383	Apr 26, 2021 (155)
45	EVA	ss3986229042	Apr 26, 2021 (155)
46	TOPMED	ss4554921801	Apr 26, 2021 (155)
47	EVA	ss5237638983	Oct 13, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5253122899	Oct 13, 2022 (156)
49	TRAN_CS_UWATERLOO	ss5314406233	Oct 13, 2022 (156)
50	EVA	ss5338030515	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5452615758	Oct 13, 2022 (156)
52	EVA	ss5506891693	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5530991714	Oct 13, 2022 (156)
54	EVA	ss5624125740	Oct 13, 2022 (156)
55	SANFORD_IMAGENETICS	ss5631584141	Oct 13, 2022 (156)
56	EVA	ss5825375359	Oct 13, 2022 (156)
57	EVA	ss5848576196	Oct 13, 2022 (156)
58	EVA	ss5853500088	Oct 13, 2022 (156)
59	EVA	ss5867716537	Oct 13, 2022 (156)
60	EVA	ss5959845950	Oct 13, 2022 (156)
61	1000Genomes	NC_000003.11 - 14180706	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000003.12 - 14139206	Oct 13, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 14180706	Oct 11, 2018 (152)
64	Genetic variation in the Estonian population	NC_000003.11 - 14180706	Oct 11, 2018 (152)
65	ExAC	NC_000003.11 - 14180706	Oct 11, 2018 (152)
66	FINRISK	NC_000003.11 - 14180706	Apr 25, 2020 (154)
67	gnomAD - Genomes	NC_000003.12 - 14139206	Apr 26, 2021 (155)
68	gnomAD - Exomes	NC_000003.11 - 14180706	Jul 13, 2019 (153)
69	GO Exome Sequencing Project	NC_000003.11 - 14180706	Oct 11, 2018 (152)
70	Genome of the Netherlands Release 5	NC_000003.11 - 14180706	Apr 25, 2020 (154)
71	Medical Genome Project healthy controls from Spanish population	NC_000003.11 - 14180706	Apr 25, 2020 (154)
72	Northern Sweden	NC_000003.11 - 14180706	Jul 13, 2019 (153)
73	The PAGE Study	NC_000003.12 - 14139206	Jul 13, 2019 (153)
74	Qatari	NC_000003.11 - 14180706	Apr 25, 2020 (154)
75	SGDP_PRJ	NC_000003.11 - 14180706	Apr 25, 2020 (154)
76	TopMed	NC_000003.12 - 14139206	Apr 26, 2021 (155)
77	UK 10K study - Twins	NC_000003.11 - 14180706	Oct 11, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000003.11 - 14180706	Jul 13, 2019 (153)
79	ALFA	NC_000003.12 - 14139206	Apr 26, 2021 (155)
80	ClinVar	RCV000039393.14	Oct 13, 2022 (156)
81	ClinVar	RCV000241757.2	Oct 13, 2022 (156)
82	ClinVar	RCV000477225.8	Oct 13, 2022 (156)
83	ClinVar	RCV000771074.2	Oct 13, 2022 (156)
84	ClinVar	RCV001650876.5	Oct 13, 2022 (156)

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
ss161929092, ss211140004, ss491829619, ss1587756367	NC_000003.10:14155706:C:T	NC_000003.12:14139205:C:T	(self)
14036644, 7782265, 5502798, 6797244, 22499, 2633370, 345204, 3416546, 124882, 2935347, 3589291, 7289246, 7782265, 1694026, ss219992319, ss342115326, ss489866466, ss536489191, ss974447128, ss978294527, ss1067448572, ss1302888771, ss1429337294, ss1584026038, ss1606460808, ss1649454841, ss1686882167, ss1711008343, ss1815616621, ss1921547361, ss1958539480, ss2021327184, ss2733561173, ss2746952031, ss2789772052, ss2991864056, ss3022214099, ss3628595596, ss3646283180, ss3652680328, ss3659764550, ss3729650482, ss3823886832, ss3825627102, ss3827672212, ss3836377991, ss3855272266, ss3984243383, ss3986229042, ss5338030515, ss5506891693, ss5624125740, ss5631584141, ss5825375359, ss5848576196, ss5959845950	NC_000003.11:14180705:C:T	NC_000003.12:14139205:C:T	(self)
RCV000039393.14, RCV000241757.2, RCV000477225.8, RCV000771074.2, RCV001650876.5, 18517649, 99637434, 233942, 392299356, 3943475827, ss2249248762, ss3708679618, ss3725992334, ss3771012473, ss3802837005, ss4554921801, ss5237638983, ss5253122899, ss5314406233, ss5452615758, ss5530991714, ss5853500088, ss5867716537	NC_000003.12:14139205:C:T	NC_000003.12:14139205:C:T	(self)
ss48423852	NT_022517.18:14120705:C:T	NC_000003.12:14139205:C:T	(self)

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

2 citations for rs35100587

PMID	Title	Author	Year	Journal
18414213	ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.	Richards CS et al.	2008	Genetics in medicine
24033266	A systematic approach to assessing the clinical significance of genetic variants.	Duzkale H et al.	2013	Clinical genetics

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs35100587