Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs45497599

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6464643 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002720 (720/264690, TOPMED)
T=0.003863 (542/140304, GnomAD)
T=0.004352 (525/120642, ExAC) (+ 12 more)
T=0.00483 (238/49260, ALFA)
T=0.00415 (54/13006, GO-ESP)
T=0.0016 (8/5008, 1000G)
T=0.0069 (31/4480, Estonian)
T=0.0042 (16/3854, ALSPAC)
T=0.0076 (28/3708, TWINSUK)
G=0.0000 (0/2922, KOREAN)
T=0.007 (7/998, GoNL)
T=0.002 (1/534, MGP)
T=0.013 (4/304, FINRISK)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
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.6464643C>G
GRCh38.p13 chr 1 NC_000001.11:g.6464643C>T
GRCh37.p13 chr 1 NC_000001.10:g.6524703C>G
GRCh37.p13 chr 1 NC_000001.10:g.6524703C>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60367G>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60367G>A
TNFRSF25 RefSeqGene NG_029910.1:g.6553G>C
TNFRSF25 RefSeqGene NG_029910.1:g.6553G>A
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+797G>C N/A Intron Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.372G>C E [GAG] > D [GAC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Glu124Asp E (Glu) > D (Asp) Missense Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.372G>A E [GAG] > E [GAA] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Glu124= E (Glu) > E (Glu) Synonymous Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.372G>C E [GAG] > D [GAC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Glu124Asp E (Glu) > D (Asp) Missense Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.372G>A E [GAG] > E [GAA] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Glu124= E (Glu) > E (Glu) Synonymous Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.372G>C E [GAG] > D [GAC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Glu124Asp E (Glu) > D (Asp) Missense Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.372G>A E [GAG] > E [GAA] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Glu124= E (Glu) > E (Glu) Synonymous Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.237G>C E [GAG] > D [GAC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Glu79Asp E (Glu) > D (Asp) Missense Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.237G>A E [GAG] > E [GAA] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Glu79= E (Glu) > E (Glu) Synonymous Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.372G>C E [GAG] > D [GAC] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Glu124Asp E (Glu) > D (Asp) Missense Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.372G>A E [GAG] > E [GAA] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Glu124= E (Glu) > E (Glu) 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 49260 C=0.99517 T=0.00483
European Sub 37246 C=0.99450 T=0.00550
African Sub 3560 C=0.9997 T=0.0003
African Others Sub 122 C=1.000 T=0.000
African American Sub 3438 C=0.9997 T=0.0003
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 500 C=0.998 T=0.002
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=0.99 T=0.01
Other Sub 7060 C=0.9958 T=0.0042


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 C=0.997280 T=0.002720
gnomAD - Genomes Global Study-wide 140304 C=0.996137 T=0.003863
gnomAD - Genomes European Sub 75964 C=0.99351 T=0.00649
gnomAD - Genomes African Sub 42062 C=0.99912 T=0.00088
gnomAD - Genomes American Sub 13666 C=0.99941 T=0.00059
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9981 T=0.0019
ExAC Global Study-wide 120642 C=0.995648 T=0.004352
ExAC Europe Sub 72734 C=0.99372 T=0.00628
ExAC Asian Sub 25138 C=0.99821 T=0.00179
ExAC American Sub 11542 C=0.99905 T=0.00095
ExAC African Sub 10332 C=0.99952 T=0.00048
ExAC Other Sub 896 C=0.992 T=0.008
GO Exome Sequencing Project Global Study-wide 13006 C=0.99585 T=0.00415
GO Exome Sequencing Project European American Sub 8600 C=0.9943 T=0.0057
GO Exome Sequencing Project African American Sub 4406 C=0.9989 T=0.0011
1000Genomes Global Study-wide 5008 C=0.9984 T=0.0016
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9950 T=0.0050
1000Genomes South Asian Sub 978 C=0.998 T=0.002
1000Genomes American Sub 694 C=0.999 T=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9931 T=0.0069
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9958 T=0.0042
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9924 T=0.0076
KOREAN population from KRGDB KOREAN Study-wide 2922 C=1.0000 G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.993 T=0.007
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
FINRISK Finnish from FINRISK project Study-wide 304 C=0.987 T=0.013
Siberian Global Study-wide 2 C=0.5 T=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 C= G T
GRCh38.p13 chr 1 NC_000001.11:g.6464643= NC_000001.11:g.6464643C>G NC_000001.11:g.6464643C>T
GRCh37.p13 chr 1 NC_000001.10:g.6524703= NC_000001.10:g.6524703C>G NC_000001.10:g.6524703C>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60367= NG_007978.1:g.60367G>C NG_007978.1:g.60367G>A
TNFRSF25 RefSeqGene NG_029910.1:g.6553= NG_029910.1:g.6553G>C NG_029910.1:g.6553G>A
TNFRSF25 transcript variant 2 NM_003790.3:c.372= NM_003790.3:c.372G>C NM_003790.3:c.372G>A
TNFRSF25 transcript variant 2 NM_003790.2:c.372= NM_003790.2:c.372G>C NM_003790.2:c.372G>A
TNFRSF25 transcript variant 1 NM_148965.2:c.372= NM_148965.2:c.372G>C NM_148965.2:c.372G>A
TNFRSF25 transcript variant 1 NM_148965.1:c.372= NM_148965.1:c.372G>C NM_148965.1:c.372G>A
TNFRSF25 transcript variant 3 NM_148966.2:c.372= NM_148966.2:c.372G>C NM_148966.2:c.372G>A
TNFRSF25 transcript variant 3 NM_148966.1:c.372= NM_148966.1:c.372G>C NM_148966.1:c.372G>A
TNFRSF25 transcript variant 4 NM_148967.2:c.237= NM_148967.2:c.237G>C NM_148967.2:c.237G>A
TNFRSF25 transcript variant 4 NM_148967.1:c.237= NM_148967.1:c.237G>C NM_148967.1:c.237G>A
TNFRSF25 transcript variant 12 NM_001039664.2:c.372= NM_001039664.2:c.372G>C NM_001039664.2:c.372G>A
TNFRSF25 transcript variant 12 NM_001039664.1:c.372= NM_001039664.1:c.372G>C NM_001039664.1:c.372G>A
TNFRSF25 transcript variant 5 NM_148968.1:c.372= NM_148968.1:c.372G>C NM_148968.1:c.372G>A
TNFRSF25 transcript variant 6 NM_148969.1:c.372= NM_148969.1:c.372G>C NM_148969.1:c.372G>A
TNFRSF25 transcript variant 8 NM_148971.1:c.372= NM_148971.1:c.372G>C NM_148971.1:c.372G>A
TNFRSF25 transcript variant 9 NM_148972.1:c.372= NM_148972.1:c.372G>C NM_148972.1:c.372G>A
TNFRSF25 transcript variant 10 NM_148973.1:c.237= NM_148973.1:c.237G>C NM_148973.1:c.237G>A
TNFRSF25 transcript variant 11 NM_148974.1:c.237= NM_148974.1:c.237G>C NM_148974.1:c.237G>A
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Glu124= NP_003781.1:p.Glu124Asp NP_003781.1:p.Glu124=
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Glu124= NP_683866.1:p.Glu124Asp NP_683866.1:p.Glu124=
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Glu124= NP_683867.1:p.Glu124Asp NP_683867.1:p.Glu124=
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Glu79= NP_683868.1:p.Glu79Asp NP_683868.1:p.Glu79=
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Glu124= NP_001034753.1:p.Glu124Asp NP_001034753.1:p.Glu124=
TNFRSF25 transcript variant 7 NM_148970.1:c.160+797= NM_148970.1:c.160+797G>C NM_148970.1:c.160+797G>A
TNFRSF25 transcript variant 7 NM_148970.2:c.160+797= NM_148970.2:c.160+797G>C NM_148970.2:c.160+797G>A
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#.

31 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss70457397 May 17, 2007 (127)
2 CANCER-GENOME ss86341806 Mar 23, 2008 (130)
3 1000GENOMES ss217314405 Jul 14, 2010 (132)
4 1000GENOMES ss230414451 Jul 14, 2010 (132)
5 NHLBI-ESP ss341928676 May 09, 2011 (134)
6 1000GENOMES ss489717694 May 04, 2012 (137)
7 CLINSEQ_SNP ss491583251 May 04, 2012 (137)
8 EVA-GONL ss974820726 Aug 21, 2014 (142)
9 1000GENOMES ss1289542647 Aug 21, 2014 (142)
10 EVA_FINRISK ss1584004194 Apr 01, 2015 (144)
11 EVA_DECODE ss1584178932 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1599475885 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1642469918 Apr 01, 2015 (144)
14 EVA_EXAC ss1685271979 Apr 01, 2015 (144)
15 EVA_MGP ss1710886360 Apr 01, 2015 (144)
16 JJLAB ss2019524943 Sep 14, 2016 (149)
17 USC_VALOUEV ss2147518264 Dec 20, 2016 (150)
18 HUMAN_LONGEVITY ss2159755150 Dec 20, 2016 (150)
19 TOPMED ss2321912281 Dec 20, 2016 (150)
20 GNOMAD ss2731072822 Nov 08, 2017 (151)
21 GNOMAD ss2746200467 Nov 08, 2017 (151)
22 GNOMAD ss2751216405 Nov 08, 2017 (151)
23 SWEGEN ss2986238942 Nov 08, 2017 (151)
24 TOPMED ss3067669969 Nov 08, 2017 (151)
25 EGCUT_WGS ss3654338940 Jul 12, 2019 (153)
26 EVA_DECODE ss3686092727 Jul 12, 2019 (153)
27 EVA ss3823553114 Apr 25, 2020 (154)
28 EVA ss3825551843 Apr 25, 2020 (154)
29 KRGDB ss3892987899 Apr 25, 2020 (154)
30 EVA ss3986096307 Apr 25, 2021 (155)
31 TOPMED ss4438024161 Apr 25, 2021 (155)
32 1000Genomes NC_000001.10 - 6524703 Oct 11, 2018 (152)
33 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 6524703 Oct 11, 2018 (152)
34 Genetic variation in the Estonian population NC_000001.10 - 6524703 Oct 11, 2018 (152)
35 ExAC NC_000001.10 - 6524703 Oct 11, 2018 (152)
36 FINRISK NC_000001.10 - 6524703 Apr 25, 2020 (154)
37 gnomAD - Genomes NC_000001.11 - 6464643 Apr 25, 2021 (155)
38 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 87380 (NC_000001.10:6524702:C:C 251027/251028, NC_000001.10:6524702:C:G 1/251028)
Row 87381 (NC_000001.10:6524702:C:C 249927/251028, NC_000001.10:6524702:C:T 1101/251028)

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

Submission ignored due to conflicting rows:
Row 87380 (NC_000001.10:6524702:C:C 251027/251028, NC_000001.10:6524702:C:G 1/251028)
Row 87381 (NC_000001.10:6524702:C:C 249927/251028, NC_000001.10:6524702:C:T 1101/251028)

- Jul 12, 2019 (153)
40 GO Exome Sequencing Project NC_000001.10 - 6524703 Oct 11, 2018 (152)
41 Genome of the Netherlands Release 5 NC_000001.10 - 6524703 Apr 25, 2020 (154)
42 KOREAN population from KRGDB NC_000001.10 - 6524703 Apr 25, 2020 (154)
43 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 6524703 Apr 25, 2020 (154)
44 Siberian NC_000001.10 - 6524703 Apr 25, 2020 (154)
45 TopMed NC_000001.11 - 6464643 Apr 25, 2021 (155)
46 UK 10K study - Twins NC_000001.10 - 6524703 Oct 11, 2018 (152)
47 ALFA NC_000001.11 - 6464643 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).

Associated ID History Updated (Build)
rs61749271 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
165293, ss2731072822, ss3892987899 NC_000001.10:6524702:C:G NC_000001.11:6464642:C:G (self)
ss217314405, ss491583251, ss1584178932 NC_000001.9:6447289:C:T NC_000001.11:6464642:C:T (self)
213478, 106260, 77188, 4448990, 655, 11846, 46422, 3112, 34618, 106260, ss230414451, ss341928676, ss489717694, ss974820726, ss1289542647, ss1584004194, ss1599475885, ss1642469918, ss1685271979, ss1710886360, ss2019524943, ss2147518264, ss2321912281, ss2731072822, ss2746200467, ss2751216405, ss2986238942, ss3654338940, ss3823553114, ss3825551843, ss3986096307 NC_000001.10:6524702:C:T NC_000001.11:6464642:C:T (self)
1469489, 1021497, 1630496, 4465142739, ss2159755150, ss3067669969, ss3686092727, ss4438024161 NC_000001.11:6464642:C:T NC_000001.11:6464642:C:T (self)
ss70457397, ss86341806 NT_021937.19:2529434:C:T NC_000001.11:6464642:C:T (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 rs45497599

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