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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.

rs34817737

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6464595 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.008395 (2222/264690, TOPMED)
C=0.001957 (491/250932, GnomAD_exome)
C=0.007973 (1118/140216, GnomAD) (+ 7 more)
C=0.002285 (275/120336, ExAC)
C=0.00272 (160/58840, ALFA)
C=0.00877 (114/13006, GO-ESP)
C=0.0080 (40/5008, 1000G)
C=0.005 (1/216, Qatari)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TNFRSF25 : Synonymous 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.6464595T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524655T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60415A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6601A>G
Gene: TNFRSF25, TNF receptor superfamily member 25 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TNFRSF25 transcript variant 7 NM_148970.2:c.160+845A>G N/A Intron Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.420A>G P [CCA] > P [CCG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Pro140= P (Pro) > P (Pro) Synonymous Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.420A>G P [CCA] > P [CCG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Pro140= P (Pro) > P (Pro) Synonymous Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.420A>G P [CCA] > P [CCG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Pro140= P (Pro) > P (Pro) Synonymous Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.285A>G P [CCA] > P [CCG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Pro95= P (Pro) > P (Pro) Synonymous Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.420A>G P [CCA] > P [CCG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Pro140= P (Pro) > P (Pro) 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.

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 58840 T=0.99728 C=0.00272
European Sub 43288 T=0.99995 C=0.00005
African Sub 6386 T=0.9779 C=0.0221
African Others Sub 214 T=0.986 C=0.014
African American Sub 6172 T=0.9776 C=0.0224
Asian Sub 184 T=1.000 C=0.000
East Asian Sub 126 T=1.000 C=0.000
Other Asian Sub 58 T=1.00 C=0.00
Latin American 1 Sub 522 T=0.992 C=0.008
Latin American 2 Sub 718 T=0.999 C=0.001
South Asian Sub 114 T=1.000 C=0.000
Other Sub 7628 T=0.9984 C=0.0016


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 T=0.991605 C=0.008395
gnomAD - Exomes Global Study-wide 250932 T=0.998043 C=0.001957
gnomAD - Exomes European Sub 134954 T=0.999933 C=0.000067
gnomAD - Exomes Asian Sub 48998 T=0.99998 C=0.00002
gnomAD - Exomes American Sub 34570 T=0.99838 C=0.00162
gnomAD - Exomes African Sub 16226 T=0.97405 C=0.02595
gnomAD - Exomes Ashkenazi Jewish Sub 10058 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6126 T=0.9993 C=0.0007
gnomAD - Genomes Global Study-wide 140216 T=0.992027 C=0.007973
gnomAD - Genomes European Sub 75938 T=0.99992 C=0.00008
gnomAD - Genomes African Sub 42020 T=0.97470 C=0.02530
gnomAD - Genomes American Sub 13660 T=0.99700 C=0.00300
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3124 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9963 C=0.0037
ExAC Global Study-wide 120336 T=0.997715 C=0.002285
ExAC Europe Sub 72524 T=0.99994 C=0.00006
ExAC Asian Sub 25112 T=1.00000 C=0.00000
ExAC American Sub 11518 T=0.99861 C=0.00139
ExAC African Sub 10288 T=0.97531 C=0.02469
ExAC Other Sub 894 T=0.999 C=0.001
Allele Frequency Aggregator Total Global 58840 T=0.99728 C=0.00272
Allele Frequency Aggregator European Sub 43288 T=0.99995 C=0.00005
Allele Frequency Aggregator Other Sub 7628 T=0.9984 C=0.0016
Allele Frequency Aggregator African Sub 6386 T=0.9779 C=0.0221
Allele Frequency Aggregator Latin American 2 Sub 718 T=0.999 C=0.001
Allele Frequency Aggregator Latin American 1 Sub 522 T=0.992 C=0.008
Allele Frequency Aggregator Asian Sub 184 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 114 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99123 C=0.00877
GO Exome Sequencing Project European American Sub 8600 T=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9741 C=0.0259
1000Genomes Global Study-wide 5008 T=0.9920 C=0.0080
1000Genomes African Sub 1322 T=0.9705 C=0.0295
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.999 C=0.001
Qatari Global Study-wide 216 T=0.995 C=0.005
SGDP_PRJ Global Study-wide 4 T=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 T= C
GRCh38.p13 chr 1 NC_000001.11:g.6464595= NC_000001.11:g.6464595T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524655= NC_000001.10:g.6524655T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60415= NG_007978.1:g.60415A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6601= NG_029910.1:g.6601A>G
TNFRSF25 transcript variant 2 NM_003790.3:c.420= NM_003790.3:c.420A>G
TNFRSF25 transcript variant 2 NM_003790.2:c.420= NM_003790.2:c.420A>G
TNFRSF25 transcript variant 1 NM_148965.2:c.420= NM_148965.2:c.420A>G
TNFRSF25 transcript variant 1 NM_148965.1:c.420= NM_148965.1:c.420A>G
TNFRSF25 transcript variant 3 NM_148966.2:c.420= NM_148966.2:c.420A>G
TNFRSF25 transcript variant 3 NM_148966.1:c.420= NM_148966.1:c.420A>G
TNFRSF25 transcript variant 4 NM_148967.2:c.285= NM_148967.2:c.285A>G
TNFRSF25 transcript variant 4 NM_148967.1:c.285= NM_148967.1:c.285A>G
TNFRSF25 transcript variant 12 NM_001039664.2:c.420= NM_001039664.2:c.420A>G
TNFRSF25 transcript variant 12 NM_001039664.1:c.420= NM_001039664.1:c.420A>G
TNFRSF25 transcript variant 5 NM_148968.1:c.420= NM_148968.1:c.420A>G
TNFRSF25 transcript variant 6 NM_148969.1:c.420= NM_148969.1:c.420A>G
TNFRSF25 transcript variant 8 NM_148971.1:c.420= NM_148971.1:c.420A>G
TNFRSF25 transcript variant 9 NM_148972.1:c.420= NM_148972.1:c.420A>G
TNFRSF25 transcript variant 10 NM_148973.1:c.285= NM_148973.1:c.285A>G
TNFRSF25 transcript variant 11 NM_148974.1:c.285= NM_148974.1:c.285A>G
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Pro140= NP_003781.1:p.Pro140=
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Pro140= NP_683866.1:p.Pro140=
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Pro140= NP_683867.1:p.Pro140=
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Pro95= NP_683868.1:p.Pro95=
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Pro140= NP_001034753.1:p.Pro140=
TNFRSF25 transcript variant 7 NM_148970.1:c.160+845= NM_148970.1:c.160+845A>G
TNFRSF25 transcript variant 7 NM_148970.2:c.160+845= NM_148970.2:c.160+845A>G
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#.

32 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48420536 Mar 14, 2006 (126)
2 EGP_SNPS ss70457398 May 17, 2007 (127)
3 1000GENOMES ss217405844 Jul 14, 2010 (132)
4 1000GENOMES ss217410992 Jul 14, 2010 (132)
5 1000GENOMES ss218218075 Jul 14, 2010 (132)
6 NHLBI-ESP ss341928671 May 09, 2011 (134)
7 ILLUMINA ss480840465 May 04, 2012 (137)
8 ILLUMINA ss482381081 May 04, 2012 (137)
9 1000GENOMES ss489717690 May 04, 2012 (137)
10 ILLUMINA ss533976413 Sep 08, 2015 (146)
11 ILLUMINA ss779233835 Sep 08, 2015 (146)
12 ILLUMINA ss781331401 Sep 08, 2015 (146)
13 ILLUMINA ss834700022 Sep 08, 2015 (146)
14 JMKIDD_LAB ss1067415446 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1067645526 Aug 21, 2014 (142)
16 1000GENOMES ss1289542644 Aug 21, 2014 (142)
17 EVA_EXAC ss1685271972 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1918018211 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2159755148 Dec 20, 2016 (150)
20 TOPMED ss2321912279 Dec 20, 2016 (150)
21 ILLUMINA ss2632472446 Nov 08, 2017 (151)
22 GNOMAD ss2731072810 Nov 08, 2017 (151)
23 GNOMAD ss2746200464 Nov 08, 2017 (151)
24 GNOMAD ss2751216402 Nov 08, 2017 (151)
25 TOPMED ss3067669964 Nov 08, 2017 (151)
26 ILLUMINA ss3626017895 Oct 11, 2018 (152)
27 ILLUMINA ss3630511487 Oct 11, 2018 (152)
28 KHV_HUMAN_GENOMES ss3798806747 Jul 12, 2019 (153)
29 EVA ss3823553112 Apr 25, 2020 (154)
30 SGDP_PRJ ss3848120391 Apr 25, 2020 (154)
31 EVA ss3986096305 Apr 25, 2021 (155)
32 TOPMED ss4438024154 Apr 25, 2021 (155)
33 1000Genomes NC_000001.10 - 6524655 Oct 11, 2018 (152)
34 ExAC NC_000001.10 - 6524655 Oct 11, 2018 (152)
35 gnomAD - Genomes NC_000001.11 - 6464595 Apr 25, 2021 (155)
36 gnomAD - Exomes NC_000001.10 - 6524655 Jul 12, 2019 (153)
37 GO Exome Sequencing Project NC_000001.10 - 6524655 Oct 11, 2018 (152)
38 Qatari NC_000001.10 - 6524655 Apr 25, 2020 (154)
39 SGDP_PRJ NC_000001.10 - 6524655 Apr 25, 2020 (154)
40 TopMed NC_000001.11 - 6464595 Apr 25, 2021 (155)
41 ALFA NC_000001.11 - 6464595 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
ss217405844, ss217410992, ss482381081 NC_000001.9:6447241:T:C NC_000001.11:6464594:T:C (self)
213475, 4448983, 87369, 11844, 60141, 137371, ss218218075, ss341928671, ss480840465, ss489717690, ss533976413, ss779233835, ss781331401, ss834700022, ss1067415446, ss1067645526, ss1289542644, ss1685271972, ss1918018211, ss2321912279, ss2632472446, ss2731072810, ss2746200464, ss2751216402, ss3626017895, ss3630511487, ss3823553112, ss3848120391, ss3986096305 NC_000001.10:6524654:T:C NC_000001.11:6464594:T:C (self)
1469484, 1021492, 1630489, 140520434, ss2159755148, ss3067669964, ss3798806747, ss4438024154 NC_000001.11:6464594:T:C NC_000001.11:6464594:T:C (self)
ss48420536, ss70457398 NT_021937.19:2529386:T:C NC_000001.11:6464594:T: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 rs34817737

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