Name: rs1886529
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.

rs1886529

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:23641505 (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=0.132022 (34945/264690, TOPMED)
G=0.120602 (16873/139906, GnomAD)
G=0.30869 (8723/28258, 14KJPN) (+ 16 more)
G=0.12353 (2309/18692, ALFA)
G=0.30805 (5163/16760, 8.3KJPN)
G=0.1597 (1023/6404, 1000G_30x)
G=0.1613 (808/5008, 1000G)
G=0.1237 (554/4480, Estonian)
G=0.1448 (558/3854, ALSPAC)
G=0.1610 (597/3708, TWINSUK)
G=0.3362 (985/2930, KOREAN)
G=0.3324 (609/1832, Korea1K)
G=0.147 (147/998, GoNL)
G=0.137 (82/600, NorthernSweden)
G=0.111 (24/216, Qatari)
G=0.224 (48/214, Vietnamese)
A=0.384 (76/198, SGDP_PRJ)
G=0.20 (8/40, GENOME_DK)
A=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TNFRSF19 : 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	18692	A=0.87647	C=0.00000, G=0.12353
European	Sub	14112	A=0.86515	C=0.00000, G=0.13485
African	Sub	2922	A=0.9784	C=0.0000, G=0.0216
African Others	Sub	114	A=0.991	C=0.000, G=0.009
African American	Sub	2808	A=0.9779	C=0.0000, G=0.0221
Asian	Sub	112	A=0.732	C=0.000, G=0.268
East Asian	Sub	86	A=0.71	C=0.00, G=0.29
Other Asian	Sub	26	A=0.81	C=0.00, G=0.19
Latin American 1	Sub	146	A=0.856	C=0.000, G=0.144
Latin American 2	Sub	610	A=0.721	C=0.000, G=0.279
South Asian	Sub	98	A=0.81	C=0.00, G=0.19
Other	Sub	692	A=0.851	C=0.000, G=0.149

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=0.867978	G=0.132022
gnomAD - Genomes	Global	Study-wide	139906	A=0.879398	G=0.120602
gnomAD - Genomes	European	Sub	75788	A=0.85544	G=0.14456
gnomAD - Genomes	African	Sub	41914	A=0.96922	G=0.03078
gnomAD - Genomes	American	Sub	13622	A=0.77470	G=0.22530
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.8419	G=0.1581
gnomAD - Genomes	East Asian	Sub	3118	A=0.7700	G=0.2300
gnomAD - Genomes	Other	Sub	2144	A=0.8526	G=0.1474
14KJPN	JAPANESE	Study-wide	28258	A=0.69131	G=0.30869
Allele Frequency Aggregator	Total	Global	18692	A=0.87647	C=0.00000, G=0.12353
Allele Frequency Aggregator	European	Sub	14112	A=0.86515	C=0.00000, G=0.13485
Allele Frequency Aggregator	African	Sub	2922	A=0.9784	C=0.0000, G=0.0216
Allele Frequency Aggregator	Other	Sub	692	A=0.851	C=0.000, G=0.149
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.721	C=0.000, G=0.279
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.856	C=0.000, G=0.144
Allele Frequency Aggregator	Asian	Sub	112	A=0.732	C=0.000, G=0.268
Allele Frequency Aggregator	South Asian	Sub	98	A=0.81	C=0.00, G=0.19
8.3KJPN	JAPANESE	Study-wide	16760	A=0.69195	G=0.30805
1000Genomes_30x	Global	Study-wide	6404	A=0.8403	G=0.1597
1000Genomes_30x	African	Sub	1786	A=0.9950	G=0.0050
1000Genomes_30x	Europe	Sub	1266	A=0.8341	G=0.1659
1000Genomes_30x	South Asian	Sub	1202	A=0.7404	G=0.2596
1000Genomes_30x	East Asian	Sub	1170	A=0.7761	G=0.2239
1000Genomes_30x	American	Sub	980	A=0.765	G=0.235
1000Genomes	Global	Study-wide	5008	A=0.8387	G=0.1613
1000Genomes	African	Sub	1322	A=0.9947	G=0.0053
1000Genomes	East Asian	Sub	1008	A=0.7738	G=0.2262
1000Genomes	Europe	Sub	1006	A=0.8340	G=0.1660
1000Genomes	South Asian	Sub	978	A=0.743	G=0.257
1000Genomes	American	Sub	694	A=0.777	G=0.223
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8763	G=0.1237
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8552	G=0.1448
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8390	G=0.1610
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6638	G=0.3362
Korean Genome Project	KOREAN	Study-wide	1832	A=0.6676	G=0.3324
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.853	G=0.147
Northern Sweden	ACPOP	Study-wide	600	A=0.863	G=0.137
Qatari	Global	Study-wide	216	A=0.889	G=0.111
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.776	G=0.224
SGDP_PRJ	Global	Study-wide	198	A=0.384	G=0.616
The Danish reference pan genome	Danish	Study-wide	40	A=0.80	G=0.20
Siberian	Global	Study-wide	18	A=0.44	G=0.56

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 13	NC_000013.11:g.23641505A>C
GRCh38.p14 chr 13	NC_000013.11:g.23641505A>G
GRCh37.p13 chr 13	NC_000013.10:g.24215644A>C
GRCh37.p13 chr 13	NC_000013.10:g.24215644A>G

Gene: TNFRSF19, TNF receptor superfamily member 19 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TNFRSF19 transcript variant 3	NM_001204458.3:c.445+1471… NM_001204458.3:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant 4	NM_001204459.2:c.49+14713… NM_001204459.2:c.49+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant 5	NM_001354985.2:c.445+1471… NM_001354985.2:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant 1	NM_018647.5:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant 2	NM_148957.4:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant X3	XM_005266446.3:c.445+1471… XM_005266446.3:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant X1	XM_047430440.1:c.445+1471… XM_047430440.1:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant X2	XM_047430441.1:c.445+1471… XM_047430441.1:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant X4	XM_047430442.1:c.445+1471… XM_047430442.1:c.445+14713A>C	N/A	Intron Variant
TNFRSF19 transcript variant X5	XM_047430443.1:c.445+1471… XM_047430443.1:c.445+14713A>C	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=	C	G
GRCh38.p14 chr 13	NC_000013.11:g.23641505=	NC_000013.11:g.23641505A>C	NC_000013.11:g.23641505A>G
GRCh37.p13 chr 13	NC_000013.10:g.24215644=	NC_000013.10:g.24215644A>C	NC_000013.10:g.24215644A>G
TNFRSF19 transcript variant 3	NM_001204458.1:c.445+14713=	NM_001204458.1:c.445+14713A>C	NM_001204458.1:c.445+14713A>G
TNFRSF19 transcript variant 3	NM_001204458.3:c.445+14713=	NM_001204458.3:c.445+14713A>C	NM_001204458.3:c.445+14713A>G
TNFRSF19 transcript variant 4	NM_001204459.1:c.49+14713=	NM_001204459.1:c.49+14713A>C	NM_001204459.1:c.49+14713A>G
TNFRSF19 transcript variant 4	NM_001204459.2:c.49+14713=	NM_001204459.2:c.49+14713A>C	NM_001204459.2:c.49+14713A>G
TNFRSF19 transcript variant 5	NM_001354985.2:c.445+14713=	NM_001354985.2:c.445+14713A>C	NM_001354985.2:c.445+14713A>G
TNFRSF19 transcript variant 1	NM_018647.3:c.445+14713=	NM_018647.3:c.445+14713A>C	NM_018647.3:c.445+14713A>G
TNFRSF19 transcript variant 1	NM_018647.5:c.445+14713=	NM_018647.5:c.445+14713A>C	NM_018647.5:c.445+14713A>G
TNFRSF19 transcript variant 2	NM_148957.3:c.445+14713=	NM_148957.3:c.445+14713A>C	NM_148957.3:c.445+14713A>G
TNFRSF19 transcript variant 2	NM_148957.4:c.445+14713=	NM_148957.4:c.445+14713A>C	NM_148957.4:c.445+14713A>G
TNFRSF19 transcript variant X1	XM_005266445.1:c.445+14713=	XM_005266445.1:c.445+14713A>C	XM_005266445.1:c.445+14713A>G
TNFRSF19 transcript variant X4	XM_005266446.1:c.445+14713=	XM_005266446.1:c.445+14713A>C	XM_005266446.1:c.445+14713A>G
TNFRSF19 transcript variant X3	XM_005266446.3:c.445+14713=	XM_005266446.3:c.445+14713A>C	XM_005266446.3:c.445+14713A>G
TNFRSF19 transcript variant X1	XM_047430440.1:c.445+14713=	XM_047430440.1:c.445+14713A>C	XM_047430440.1:c.445+14713A>G
TNFRSF19 transcript variant X2	XM_047430441.1:c.445+14713=	XM_047430441.1:c.445+14713A>C	XM_047430441.1:c.445+14713A>G
TNFRSF19 transcript variant X4	XM_047430442.1:c.445+14713=	XM_047430442.1:c.445+14713A>C	XM_047430442.1:c.445+14713A>G
TNFRSF19 transcript variant X5	XM_047430443.1:c.445+14713=	XM_047430443.1:c.445+14713A>C	XM_047430443.1:c.445+14713A>G

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#.

61 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2766301	Jan 12, 2001 (92)
2	SC_SNP	ss13259082	Dec 05, 2003 (119)
3	ABI	ss40295620	Mar 14, 2006 (126)
4	HGSV	ss77662467	Dec 07, 2007 (129)
5	BCMHGSC_JDW	ss89529563	Mar 24, 2008 (129)
6	BGI	ss103102061	Dec 01, 2009 (131)
7	ENSEMBL	ss133480530	Dec 01, 2009 (131)
8	GMI	ss154522768	Dec 01, 2009 (131)
9	BCM-HGSC-SUB	ss208714024	Jul 04, 2010 (132)
10	1000GENOMES	ss236173281	Jul 15, 2010 (132)
11	1000GENOMES	ss242684459	Jul 15, 2010 (132)
12	GMI	ss281635661	May 04, 2012 (137)
13	GMI	ss286666548	Apr 25, 2013 (138)
14	PJP	ss291555272	May 09, 2011 (134)
15	SSMP	ss659138853	Apr 25, 2013 (138)
16	EVA-GONL	ss990185292	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1078931850	Aug 21, 2014 (142)
18	1000GENOMES	ss1347468894	Aug 21, 2014 (142)
19	DDI	ss1427125328	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1576667511	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1629876320	Apr 01, 2015 (144)
22	EVA_DECODE	ss1642291234	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1672870353	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1933553098	Feb 12, 2016 (147)
25	JJLAB	ss2027530643	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2155894124	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2194822118	Dec 20, 2016 (150)
28	SYSTEMSBIOZJU	ss2628252609	Nov 08, 2017 (151)
29	GRF	ss2700265277	Nov 08, 2017 (151)
30	GNOMAD	ss2917530049	Nov 08, 2017 (151)
31	SWEGEN	ss3010709651	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3027579651	Nov 08, 2017 (151)
33	CSHL	ss3350361041	Nov 08, 2017 (151)
34	EGCUT_WGS	ss3677977069	Jul 13, 2019 (153)
35	EVA_DECODE	ss3694912031	Jul 13, 2019 (153)
36	ACPOP	ss3739575930	Jul 13, 2019 (153)
37	EVA	ss3751226846	Jul 13, 2019 (153)
38	PACBIO	ss3787401238	Jul 13, 2019 (153)
39	PACBIO	ss3792475399	Jul 13, 2019 (153)
40	PACBIO	ss3797359092	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3816557932	Jul 13, 2019 (153)
42	EVA	ss3833443951	Apr 27, 2020 (154)
43	EVA	ss3840297556	Apr 27, 2020 (154)
44	EVA	ss3845781927	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3879578917	Apr 27, 2020 (154)
46	KRGDB	ss3928394737	Apr 27, 2020 (154)
47	KOGIC	ss3973194232	Apr 27, 2020 (154)
48	TOPMED	ss4939745608	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5209149225	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5293073171	Oct 16, 2022 (156)
51	EVA	ss5409568867	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5487503824	Oct 16, 2022 (156)
53	EVA	ss5510905212	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5591698236	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5654387063	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5760782803	Oct 16, 2022 (156)
57	YY_MCH	ss5813942814	Oct 16, 2022 (156)
58	EVA	ss5839211803	Oct 16, 2022 (156)
59	EVA	ss5850644130	Oct 16, 2022 (156)
60	EVA	ss5924344621	Oct 16, 2022 (156)
61	EVA	ss5945792423	Oct 16, 2022 (156)
62	1000Genomes	NC_000013.10 - 24215644	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000013.11 - 23641505	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 24215644	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000013.10 - 24215644	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000013.10 - 24215644	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000013.11 - 23641505	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000013.10 - 24215644	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000013.10 - 24215644	Apr 27, 2020 (154)
70	Korean Genome Project	NC_000013.11 - 23641505	Apr 27, 2020 (154)
71	Northern Sweden	NC_000013.10 - 24215644	Jul 13, 2019 (153)
72	Qatari	NC_000013.10 - 24215644	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000013.10 - 24215644	Apr 27, 2020 (154)
74	Siberian	NC_000013.10 - 24215644	Apr 27, 2020 (154)
75	8.3KJPN	NC_000013.10 - 24215644	Apr 26, 2021 (155)
76	14KJPN	NC_000013.11 - 23641505	Oct 16, 2022 (156)
77	TopMed	NC_000013.11 - 23641505	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000013.10 - 24215644	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000013.10 - 24215644	Jul 13, 2019 (153)
80	ALFA	NC_000013.11 - 23641505	Apr 26, 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
3881617392	NC_000013.11:23641504:A:C	NC_000013.11:23641504:A:C	(self)
ss77662467, ss89529563, ss208714024, ss281635661, ss286666548, ss291555272, ss1642291234	NC_000013.9:23113643:A:G	NC_000013.11:23641504:A:G	(self)
60311221, 33494332, 23715317, 3216675, 14943005, 35572131, 12860795, 15595028, 31595897, 8410478, 67118532, 33494332, 7429434, ss236173281, ss242684459, ss659138853, ss990185292, ss1078931850, ss1347468894, ss1427125328, ss1576667511, ss1629876320, ss1672870353, ss1933553098, ss2027530643, ss2155894124, ss2628252609, ss2700265277, ss2917530049, ss3010709651, ss3350361041, ss3677977069, ss3739575930, ss3751226846, ss3787401238, ss3792475399, ss3797359092, ss3833443951, ss3840297556, ss3879578917, ss3928394737, ss5209149225, ss5409568867, ss5510905212, ss5654387063, ss5839211803, ss5945792423	NC_000013.10:24215643:A:G	NC_000013.11:23641504:A:G	(self)
79224171, 425341104, 29572233, 94619907, 155291266, 3881617392, ss2194822118, ss3027579651, ss3694912031, ss3816557932, ss3845781927, ss3973194232, ss4939745608, ss5293073171, ss5487503824, ss5591698236, ss5760782803, ss5813942814, ss5850644130, ss5924344621	NC_000013.11:23641504:A:G	NC_000013.11:23641504:A:G	(self)
ss13259082	NT_009799.12:5195643:A:G	NC_000013.11:23641504:A:G	(self)
ss2766301, ss40295620, ss103102061, ss133480530, ss154522768	NT_024524.14:5195643:A:G	NC_000013.11:23641504:A:G	(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 rs1886529

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

rs1886529