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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.

rs35137293

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6464589 (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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.006126 (736/120150, ExAC)
C=0.00472 (276/58516, ALFA)
C=0.02061 (268/13006, GO-ESP) (+ 3 more)
C=0.0208 (104/5008, 1000G)
C=0.042 (9/216, Qatari)
T=0.4 (4/10, SGDP_PRJ)
Clinical Significance
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.6464589T>A
GRCh38.p13 chr 1 NC_000001.11:g.6464589T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524649T>A
GRCh37.p13 chr 1 NC_000001.10:g.6524649T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60421A>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60421A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6607A>T
TNFRSF25 RefSeqGene NG_029910.1:g.6607A>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+851A>T N/A Intron Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.426A>T L [CTA] > L [CTT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.426A>G L [CTA] > L [CTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.426A>T L [CTA] > L [CTT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.426A>G L [CTA] > L [CTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.426A>T L [CTA] > L [CTT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.426A>G L [CTA] > L [CTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.291A>T L [CTA] > L [CTT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Leu97= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.291A>G L [CTA] > L [CTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Leu97= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.426A>T L [CTA] > L [CTT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Leu142= L (Leu) > L (Leu) Synonymous Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.426A>G L [CTA] > L [CTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Leu142= L (Leu) > L (Leu) 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.

Allele: C (allele ID: 696836 )
ClinVar Accession Disease Names Clinical Significance
RCV000958403.1 not provided Benign

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 58516 T=0.99528 A=0.00000, C=0.00472
European Sub 43236 T=0.99972 A=0.00000, C=0.00028
African Sub 6142 T=0.9634 A=0.0000, C=0.0366
African Others Sub 206 T=0.927 A=0.000, C=0.073
African American Sub 5936 T=0.9646 A=0.0000, C=0.0354
Asian Sub 184 T=1.000 A=0.000, C=0.000
East Asian Sub 126 T=1.000 A=0.000, C=0.000
Other Asian Sub 58 T=1.00 A=0.00, C=0.00
Latin American 1 Sub 520 T=0.979 A=0.000, C=0.021
Latin American 2 Sub 714 T=0.999 A=0.000, C=0.001
South Asian Sub 114 T=1.000 A=0.000, C=0.000
Other Sub 7606 T=0.9965 A=0.0000, C=0.0035


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
ExAC Global Study-wide 120150 T=0.993874 C=0.006126
ExAC Europe Sub 72390 T=0.99983 C=0.00017
ExAC Asian Sub 25094 T=0.99996 C=0.00004
ExAC American Sub 11504 T=0.99661 C=0.00339
ExAC African Sub 10268 T=0.93387 C=0.06613
ExAC Other Sub 894 T=0.994 C=0.006
GO Exome Sequencing Project Global Study-wide 13006 T=0.97939 C=0.02061
GO Exome Sequencing Project European American Sub 8600 T=0.9993 C=0.0007
GO Exome Sequencing Project African American Sub 4406 T=0.9405 C=0.0595
1000Genomes Global Study-wide 5008 T=0.9792 C=0.0208
1000Genomes African Sub 1322 T=0.9266 C=0.0734
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9980 C=0.0020
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.993 C=0.007
Qatari Global Study-wide 216 T=0.958 C=0.042
SGDP_PRJ Global Study-wide 10 T=0.4 C=0.6
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= A C
GRCh38.p13 chr 1 NC_000001.11:g.6464589= NC_000001.11:g.6464589T>A NC_000001.11:g.6464589T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524649= NC_000001.10:g.6524649T>A NC_000001.10:g.6524649T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60421= NG_007978.1:g.60421A>T NG_007978.1:g.60421A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6607= NG_029910.1:g.6607A>T NG_029910.1:g.6607A>G
TNFRSF25 transcript variant 2 NM_003790.3:c.426= NM_003790.3:c.426A>T NM_003790.3:c.426A>G
TNFRSF25 transcript variant 2 NM_003790.2:c.426= NM_003790.2:c.426A>T NM_003790.2:c.426A>G
TNFRSF25 transcript variant 1 NM_148965.2:c.426= NM_148965.2:c.426A>T NM_148965.2:c.426A>G
TNFRSF25 transcript variant 1 NM_148965.1:c.426= NM_148965.1:c.426A>T NM_148965.1:c.426A>G
TNFRSF25 transcript variant 3 NM_148966.2:c.426= NM_148966.2:c.426A>T NM_148966.2:c.426A>G
TNFRSF25 transcript variant 3 NM_148966.1:c.426= NM_148966.1:c.426A>T NM_148966.1:c.426A>G
TNFRSF25 transcript variant 4 NM_148967.2:c.291= NM_148967.2:c.291A>T NM_148967.2:c.291A>G
TNFRSF25 transcript variant 4 NM_148967.1:c.291= NM_148967.1:c.291A>T NM_148967.1:c.291A>G
TNFRSF25 transcript variant 12 NM_001039664.2:c.426= NM_001039664.2:c.426A>T NM_001039664.2:c.426A>G
TNFRSF25 transcript variant 12 NM_001039664.1:c.426= NM_001039664.1:c.426A>T NM_001039664.1:c.426A>G
TNFRSF25 transcript variant 5 NM_148968.1:c.426= NM_148968.1:c.426A>T NM_148968.1:c.426A>G
TNFRSF25 transcript variant 6 NM_148969.1:c.426= NM_148969.1:c.426A>T NM_148969.1:c.426A>G
TNFRSF25 transcript variant 8 NM_148971.1:c.426= NM_148971.1:c.426A>T NM_148971.1:c.426A>G
TNFRSF25 transcript variant 9 NM_148972.1:c.426= NM_148972.1:c.426A>T NM_148972.1:c.426A>G
TNFRSF25 transcript variant 10 NM_148973.1:c.291= NM_148973.1:c.291A>T NM_148973.1:c.291A>G
TNFRSF25 transcript variant 11 NM_148974.1:c.291= NM_148974.1:c.291A>T NM_148974.1:c.291A>G
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Leu142= NP_003781.1:p.Leu142= NP_003781.1:p.Leu142=
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Leu142= NP_683866.1:p.Leu142= NP_683866.1:p.Leu142=
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Leu142= NP_683867.1:p.Leu142= NP_683867.1:p.Leu142=
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Leu97= NP_683868.1:p.Leu97= NP_683868.1:p.Leu97=
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Leu142= NP_001034753.1:p.Leu142= NP_001034753.1:p.Leu142=
TNFRSF25 transcript variant 7 NM_148970.1:c.160+851= NM_148970.1:c.160+851A>T NM_148970.1:c.160+851A>G
TNFRSF25 transcript variant 7 NM_148970.2:c.160+851= NM_148970.2:c.160+851A>T NM_148970.2:c.160+851A>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#.

40 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48420537 Mar 14, 2006 (126)
2 EGP_SNPS ss70457399 May 17, 2007 (127)
3 BUSHMAN ss197965738 Jul 04, 2010 (132)
4 1000GENOMES ss217405838 Jul 14, 2010 (132)
5 1000GENOMES ss217410494 Jul 14, 2010 (132)
6 1000GENOMES ss217410984 Jul 14, 2010 (132)
7 1000GENOMES ss218218074 Jul 14, 2010 (132)
8 NHLBI-ESP ss341928670 May 09, 2011 (134)
9 ILLUMINA ss480956522 May 04, 2012 (137)
10 ILLUMINA ss482381078 May 04, 2012 (137)
11 1000GENOMES ss489717688 May 04, 2012 (137)
12 ILLUMINA ss534046408 Sep 08, 2015 (146)
13 TISHKOFF ss553757167 Apr 25, 2013 (138)
14 ILLUMINA ss780644173 Sep 08, 2015 (146)
15 ILLUMINA ss781360670 Aug 21, 2014 (142)
16 ILLUMINA ss783599512 Sep 08, 2015 (146)
17 ILLUMINA ss836138695 Sep 08, 2015 (146)
18 JMKIDD_LAB ss1067415445 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067645525 Aug 21, 2014 (142)
20 1000GENOMES ss1289542643 Aug 21, 2014 (142)
21 EVA_EXAC ss1685271971 Apr 01, 2015 (144)
22 HAMMER_LAB ss1793836953 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1918018210 Feb 12, 2016 (147)
24 HUMAN_LONGEVITY ss2159755147 Dec 20, 2016 (150)
25 TOPMED ss2321912278 Dec 20, 2016 (150)
26 ILLUMINA ss2632472445 Nov 08, 2017 (151)
27 GNOMAD ss2731072809 Nov 08, 2017 (151)
28 GNOMAD ss2746200462 Nov 08, 2017 (151)
29 GNOMAD ss2751216400 Nov 08, 2017 (151)
30 TOPMED ss3067669963 Nov 08, 2017 (151)
31 ILLUMINA ss3626017894 Oct 11, 2018 (152)
32 ILLUMINA ss3630511486 Oct 11, 2018 (152)
33 KHV_HUMAN_GENOMES ss3798806746 Jul 12, 2019 (153)
34 EVA ss3823553111 Apr 25, 2020 (154)
35 EVA ss3825551841 Apr 25, 2020 (154)
36 SGDP_PRJ ss3848120390 Apr 25, 2020 (154)
37 FSA-LAB ss3983913887 Apr 25, 2021 (155)
38 EVA ss3986096304 Apr 25, 2021 (155)
39 TOPMED ss4438024152 Apr 25, 2021 (155)
40 TOPMED ss4438024153 Apr 25, 2021 (155)
41 1000Genomes NC_000001.10 - 6524649 Oct 11, 2018 (152)
42 ExAC NC_000001.10 - 6524649 Oct 11, 2018 (152)
43 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1469481 (NC_000001.11:6464588:T:A 1/140236)
Row 1469482 (NC_000001.11:6464588:T:C 2720/140236)

- Apr 25, 2021 (155)
44 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1469481 (NC_000001.11:6464588:T:A 1/140236)
Row 1469482 (NC_000001.11:6464588:T:C 2720/140236)

- Apr 25, 2021 (155)
45 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 87367 (NC_000001.10:6524648:T:T 250829/250830, NC_000001.10:6524648:T:A 1/250830)
Row 87368 (NC_000001.10:6524648:T:T 249644/250830, NC_000001.10:6524648:T:C 1186/250830)

- Jul 12, 2019 (153)
46 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 87367 (NC_000001.10:6524648:T:T 250829/250830, NC_000001.10:6524648:T:A 1/250830)
Row 87368 (NC_000001.10:6524648:T:T 249644/250830, NC_000001.10:6524648:T:C 1186/250830)

- Jul 12, 2019 (153)
47 GO Exome Sequencing Project NC_000001.10 - 6524649 Oct 11, 2018 (152)
48 Qatari NC_000001.10 - 6524649 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000001.10 - 6524649 Apr 25, 2020 (154)
50 TopMed

Submission ignored due to conflicting rows:
Row 1630487 (NC_000001.11:6464588:T:A 3/264690)
Row 1630488 (NC_000001.11:6464588:T:C 5272/264690)

- Apr 25, 2021 (155)
51 TopMed

Submission ignored due to conflicting rows:
Row 1630487 (NC_000001.11:6464588:T:A 3/264690)
Row 1630488 (NC_000001.11:6464588:T:C 5272/264690)

- Apr 25, 2021 (155)
52 ALFA NC_000001.11 - 6464589 Apr 25, 2021 (155)
53 ClinVar RCV000958403.1 Apr 25, 2020 (154)
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
ss2731072809, ss2746200462, ss2751216400 NC_000001.10:6524648:T:A NC_000001.11:6464588:T:A (self)
9693031632, ss4438024152 NC_000001.11:6464588:T:A NC_000001.11:6464588:T:A
ss197965738, ss217405838, ss217410494, ss217410984, ss482381078 NC_000001.9:6447235:T:C NC_000001.11:6464588:T:C (self)
213474, 4448982, 11843, 60140, 137370, ss218218074, ss341928670, ss480956522, ss489717688, ss534046408, ss553757167, ss780644173, ss781360670, ss783599512, ss836138695, ss1067415445, ss1067645525, ss1289542643, ss1685271971, ss1793836953, ss1918018210, ss2321912278, ss2632472445, ss2731072809, ss2746200462, ss2751216400, ss3626017894, ss3630511486, ss3823553111, ss3825551841, ss3848120390, ss3983913887, ss3986096304 NC_000001.10:6524648:T:C NC_000001.11:6464588:T:C (self)
RCV000958403.1, 1021491, 9693031632, ss2159755147, ss3067669963, ss3798806746, ss4438024153 NC_000001.11:6464588:T:C NC_000001.11:6464588:T:C (self)
ss48420537, ss70457399 NT_021937.19:2529380:T:C NC_000001.11:6464588: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 rs35137293

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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
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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