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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.

rs34529016

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6462158 (GRCh38.p13) 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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.008421 (2229/264690, TOPMED)
C=0.001979 (481/243070, GnomAD_exome)
C=0.008053 (1129/140196, GnomAD) (+ 8 more)
C=0.002343 (279/119054, ExAC)
C=0.01236 (973/78692, PAGE_STUDY)
C=0.00211 (90/42640, ALFA)
C=0.00877 (114/13006, GO-ESP)
C=0.0084 (42/5008, 1000G)
C=0.005 (1/216, Qatari)
G=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TNFRSF25 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.6462158G>C
GRCh37.p13 chr 1 NC_000001.10:g.6522218G>C
ESPN RefSeqGene (LRG_1281) NG_015866.1:g.42371G>C
TNFRSF25 RefSeqGene NG_029910.1:g.9038C>G
Gene: TNFRSF25, TNF receptor superfamily member 25 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TNFRSF25 transcript variant 12 NM_001039664.2:c. N/A Genic Downstream Transcript Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.761C>G P [CCC] > R [CGC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Pro254Arg P (Pro) > R (Arg) Missense Variant
TNFRSF25 transcript variant 7 NM_148970.2:c.212C>G P [CCC] > R [CGC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Pro71Arg P (Pro) > R (Arg) Missense Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.788C>G P [CCC] > R [CGC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Pro263Arg P (Pro) > R (Arg) Missense Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.626C>G P [CCC] > R [CGC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Pro209Arg P (Pro) > R (Arg) Missense Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.650C>G P [CCC] > R [CGC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Pro217Arg P (Pro) > R (Arg) Missense 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.

Not Reported in ClinVar

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 42640 G=0.99789 C=0.00211
European Sub 31060 G=0.99994 C=0.00006
African Sub 3574 G=0.9787 C=0.0213
African Others Sub 122 G=0.992 C=0.008
African American Sub 3452 G=0.9783 C=0.0217
Asian Sub 168 G=1.000 C=0.000
East Asian Sub 112 G=1.000 C=0.000
Other Asian Sub 56 G=1.00 C=0.00
Latin American 1 Sub 476 G=0.992 C=0.008
Latin American 2 Sub 626 G=1.000 C=0.000
South Asian Sub 98 G=1.00 C=0.00
Other Sub 6638 G=0.9988 C=0.0012


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 G=0.991579 C=0.008421
gnomAD - Exomes Global Study-wide 243070 G=0.998021 C=0.001979
gnomAD - Exomes European Sub 131510 G=0.999916 C=0.000084
gnomAD - Exomes Asian Sub 47748 G=0.99998 C=0.00002
gnomAD - Exomes American Sub 32454 G=0.99849 C=0.00151
gnomAD - Exomes African Sub 16138 G=0.97422 C=0.02578
gnomAD - Exomes Ashkenazi Jewish Sub 9354 G=1.0000 C=0.0000
gnomAD - Exomes Other Sub 5866 G=0.9993 C=0.0007
gnomAD - Genomes Global Study-wide 140196 G=0.991947 C=0.008053
gnomAD - Genomes European Sub 75916 G=0.99986 C=0.00014
gnomAD - Genomes African Sub 42008 G=0.97462 C=0.02538
gnomAD - Genomes American Sub 13662 G=0.99693 C=0.00307
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9954 C=0.0046
ExAC Global Study-wide 119054 G=0.997657 C=0.002343
ExAC Europe Sub 72520 G=0.99992 C=0.00008
ExAC Asian Sub 23742 G=1.00000 C=0.00000
ExAC American Sub 11554 G=0.99853 C=0.00147
ExAC African Sub 10344 G=0.97535 C=0.02465
ExAC Other Sub 894 G=0.999 C=0.001
The PAGE Study Global Study-wide 78692 G=0.98764 C=0.01236
The PAGE Study AfricanAmerican Sub 32514 G=0.97552 C=0.02448
The PAGE Study Mexican Sub 10808 G=0.99843 C=0.00157
The PAGE Study Asian Sub 8316 G=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 G=0.9928 C=0.0072
The PAGE Study NativeHawaiian Sub 4532 G=0.9996 C=0.0004
The PAGE Study Cuban Sub 4228 G=0.9969 C=0.0031
The PAGE Study Dominican Sub 3828 G=0.9835 C=0.0165
The PAGE Study CentralAmerican Sub 2450 G=0.9939 C=0.0061
The PAGE Study SouthAmerican Sub 1982 G=0.9960 C=0.0040
The PAGE Study NativeAmerican Sub 1260 G=0.9984 C=0.0016
The PAGE Study SouthAsian Sub 856 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 42640 G=0.99789 C=0.00211
Allele Frequency Aggregator European Sub 31060 G=0.99994 C=0.00006
Allele Frequency Aggregator Other Sub 6638 G=0.9988 C=0.0012
Allele Frequency Aggregator African Sub 3574 G=0.9787 C=0.0213
Allele Frequency Aggregator Latin American 2 Sub 626 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 476 G=0.992 C=0.008
Allele Frequency Aggregator Asian Sub 168 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.99123 C=0.00877
GO Exome Sequencing Project European American Sub 8600 G=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9741 C=0.0259
1000Genomes Global Study-wide 5008 G=0.9916 C=0.0084
1000Genomes African Sub 1322 G=0.9690 C=0.0310
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=0.999 C=0.001
Qatari Global Study-wide 216 G=0.995 C=0.005
SGDP_PRJ Global Study-wide 4 G=0.5 C=0.5
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 G= C
GRCh38.p13 chr 1 NC_000001.11:g.6462158= NC_000001.11:g.6462158G>C
GRCh37.p13 chr 1 NC_000001.10:g.6522218= NC_000001.10:g.6522218G>C
ESPN RefSeqGene (LRG_1281) NG_015866.1:g.42371= NG_015866.1:g.42371G>C
TNFRSF25 RefSeqGene NG_029910.1:g.9038= NG_029910.1:g.9038C>G
TNFRSF25 transcript variant 2 NM_003790.3:c.761= NM_003790.3:c.761C>G
TNFRSF25 transcript variant 2 NM_003790.2:c.761= NM_003790.2:c.761C>G
TNFRSF25 transcript variant 1 NM_148965.2:c.788= NM_148965.2:c.788C>G
TNFRSF25 transcript variant 1 NM_148965.1:c.788= NM_148965.1:c.788C>G
TNFRSF25 transcript variant 3 NM_148966.2:c.650= NM_148966.2:c.650C>G
TNFRSF25 transcript variant 3 NM_148966.1:c.650= NM_148966.1:c.650C>G
TNFRSF25 transcript variant 4 NM_148967.2:c.626= NM_148967.2:c.626C>G
TNFRSF25 transcript variant 4 NM_148967.1:c.626= NM_148967.1:c.626C>G
TNFRSF25 transcript variant 7 NM_148970.2:c.212= NM_148970.2:c.212C>G
TNFRSF25 transcript variant 7 NM_148970.1:c.212= NM_148970.1:c.212C>G
TNFRSF25 transcript variant 5 NM_148968.1:c.*48= NM_148968.1:c.*48C>G
TNFRSF25 transcript variant 6 NM_148969.1:c.*100= NM_148969.1:c.*100C>G
TNFRSF25 transcript variant 8 NM_148971.1:c.*48= NM_148971.1:c.*48C>G
TNFRSF25 transcript variant 9 NM_148972.1:c.*48= NM_148972.1:c.*48C>G
TNFRSF25 transcript variant 10 NM_148973.1:c.*48= NM_148973.1:c.*48C>G
TNFRSF25 transcript variant 11 NM_148974.1:c.345= NM_148974.1:c.345C>G
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Pro254= NP_003781.1:p.Pro254Arg
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Pro263= NP_683866.1:p.Pro263Arg
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Pro217= NP_683867.1:p.Pro217Arg
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Pro209= NP_683868.1:p.Pro209Arg
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Pro71= NP_683871.1:p.Pro71Arg
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#.

50 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48420539 Mar 14, 2006 (126)
2 EGP_SNPS ss70457417 May 16, 2007 (127)
3 ILLUMINA ss160622231 Dec 01, 2009 (131)
4 1000GENOMES ss217405826 Jul 14, 2010 (132)
5 1000GENOMES ss217410975 Jul 14, 2010 (132)
6 1000GENOMES ss218218068 Jul 14, 2010 (132)
7 NHLBI-ESP ss341928654 May 09, 2011 (134)
8 ILLUMINA ss481703536 Sep 08, 2015 (146)
9 1000GENOMES ss489717671 May 04, 2012 (137)
10 EXOME_CHIP ss491285322 May 04, 2012 (137)
11 ILLUMINA ss533996315 Sep 08, 2015 (146)
12 ILLUMINA ss780902057 Sep 08, 2015 (146)
13 ILLUMINA ss783589229 Sep 08, 2015 (146)
14 JMKIDD_LAB ss974432903 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1067415442 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1067645505 Aug 21, 2014 (142)
17 1000GENOMES ss1289542559 Aug 21, 2014 (142)
18 EVA_EXAC ss1685271817 Apr 01, 2015 (144)
19 ILLUMINA ss1751929335 Sep 08, 2015 (146)
20 ILLUMINA ss1917721931 Feb 12, 2016 (147)
21 WEILL_CORNELL_DGM ss1918018188 Feb 12, 2016 (147)
22 ILLUMINA ss1945983420 Feb 12, 2016 (147)
23 ILLUMINA ss1958237400 Feb 12, 2016 (147)
24 HUMAN_LONGEVITY ss2159754972 Dec 20, 2016 (150)
25 TOPMED ss2321912106 Dec 20, 2016 (150)
26 GNOMAD ss2731072568 Nov 08, 2017 (151)
27 GNOMAD ss2746200393 Nov 08, 2017 (151)
28 GNOMAD ss2751216179 Nov 08, 2017 (151)
29 AFFY ss2984843394 Nov 08, 2017 (151)
30 ILLUMINA ss3021050289 Nov 08, 2017 (151)
31 TOPMED ss3067669457 Nov 08, 2017 (151)
32 ILLUMINA ss3626017883 Oct 11, 2018 (152)
33 ILLUMINA ss3626017884 Oct 11, 2018 (152)
34 ILLUMINA ss3634304802 Oct 11, 2018 (152)
35 ILLUMINA ss3635981169 Oct 11, 2018 (152)
36 ILLUMINA ss3640012167 Oct 11, 2018 (152)
37 ILLUMINA ss3644479275 Oct 11, 2018 (152)
38 ILLUMINA ss3651373085 Oct 11, 2018 (152)
39 ILLUMINA ss3653617254 Oct 11, 2018 (152)
40 EVA_DECODE ss3686092692 Jul 12, 2019 (153)
41 ILLUMINA ss3724993020 Jul 12, 2019 (153)
42 ILLUMINA ss3744338371 Jul 12, 2019 (153)
43 ILLUMINA ss3744605781 Jul 12, 2019 (153)
44 PAGE_CC ss3770782674 Jul 12, 2019 (153)
45 ILLUMINA ss3772107432 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3798806725 Jul 12, 2019 (153)
47 EVA ss3823553068 Apr 25, 2020 (154)
48 SGDP_PRJ ss3848120356 Apr 25, 2020 (154)
49 EVA ss3986096295 Apr 25, 2021 (155)
50 TOPMED ss4438023514 Apr 25, 2021 (155)
51 1000Genomes NC_000001.10 - 6522218 Oct 11, 2018 (152)
52 ExAC NC_000001.10 - 6522218 Oct 11, 2018 (152)
53 gnomAD - Genomes NC_000001.11 - 6462158 Apr 25, 2021 (155)
54 gnomAD - Exomes NC_000001.10 - 6522218 Jul 12, 2019 (153)
55 GO Exome Sequencing Project NC_000001.10 - 6522218 Oct 11, 2018 (152)
56 The PAGE Study NC_000001.11 - 6462158 Jul 12, 2019 (153)
57 Qatari NC_000001.10 - 6522218 Apr 25, 2020 (154)
58 SGDP_PRJ NC_000001.10 - 6522218 Apr 25, 2020 (154)
59 TopMed NC_000001.11 - 6462158 Apr 25, 2021 (155)
60 ALFA NC_000001.11 - 6462158 Apr 25, 2021 (155)
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
ss217405826, ss217410975 NC_000001.9:6444804:G:C NC_000001.11:6462157:G:C (self)
213390, 4448822, 87138, 11800, 60118, 137336, ss218218068, ss341928654, ss481703536, ss489717671, ss491285322, ss533996315, ss780902057, ss783589229, ss974432903, ss1067415442, ss1067645505, ss1289542559, ss1685271817, ss1751929335, ss1917721931, ss1918018188, ss1945983420, ss1958237400, ss2321912106, ss2731072568, ss2746200393, ss2751216179, ss2984843394, ss3021050289, ss3626017883, ss3626017884, ss3634304802, ss3635981169, ss3640012167, ss3644479275, ss3651373085, ss3653617254, ss3744338371, ss3744605781, ss3772107432, ss3823553068, ss3848120356, ss3986096295 NC_000001.10:6522217:G:C NC_000001.11:6462157:G:C (self)
1468911, 4143, 1021073, 1629849, 941518582, ss2159754972, ss3067669457, ss3686092692, ss3724993020, ss3770782674, ss3798806725, ss4438023514 NC_000001.11:6462157:G:C NC_000001.11:6462157:G:C (self)
ss48420539, ss70457417, ss160622231 NT_021937.19:2526949:G:C NC_000001.11:6462157:G:C (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 rs34529016

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.post596+ae089ad