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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.

rs3170675

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6464628 (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=0.035483 (9392/264690, TOPMED)
C=0.038441 (9651/251060, GnomAD_exome)
C=0.039589 (5551/140216, GnomAD) (+ 17 more)
C=0.039611 (4779/120648, ExAC)
C=0.02135 (1680/78694, PAGE_STUDY)
C=0.04804 (2961/61640, ALFA)
C=0.03760 (489/13006, GO-ESP)
C=0.0202 (101/5008, 1000G)
C=0.0589 (264/4480, Estonian)
C=0.0607 (234/3854, ALSPAC)
C=0.0518 (192/3708, TWINSUK)
C=0.069 (69/998, GoNL)
C=0.073 (44/600, NorthernSweden)
C=0.049 (26/534, MGP)
C=0.109 (33/304, FINRISK)
C=0.05 (2/40, GENOME_DK)
T=0.5 (5/10, SGDP_PRJ)
C=0.5 (5/10, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)
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.6464628T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524688T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60382A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6568A>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+812A>G N/A Intron Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.387A>G Q [CAA] > Q [CAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Gln129= Q (Gln) > Q (Gln) Synonymous Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.387A>G Q [CAA] > Q [CAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Gln129= Q (Gln) > Q (Gln) Synonymous Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.387A>G Q [CAA] > Q [CAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Gln129= Q (Gln) > Q (Gln) Synonymous Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.252A>G Q [CAA] > Q [CAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Gln84= Q (Gln) > Q (Gln) Synonymous Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.387A>G Q [CAA] > Q [CAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Gln129= Q (Gln) > Q (Gln) 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 61640 T=0.95196 C=0.04804
European Sub 47570 T=0.94690 C=0.05310
African Sub 4200 T=0.9886 C=0.0114
African Others Sub 132 T=1.000 C=0.000
African American Sub 4068 T=0.9882 C=0.0118
Asian Sub 216 T=1.000 C=0.000
East Asian Sub 158 T=1.000 C=0.000
Other Asian Sub 58 T=1.00 C=0.00
Latin American 1 Sub 518 T=0.965 C=0.035
Latin American 2 Sub 702 T=0.960 C=0.040
South Asian Sub 120 T=0.992 C=0.008
Other Sub 8314 T=0.9591 C=0.0409


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=0.964517 C=0.035483
gnomAD - Exomes Global Study-wide 251060 T=0.961559 C=0.038441
gnomAD - Exomes European Sub 135064 T=0.939466 C=0.060534
gnomAD - Exomes Asian Sub 49000 T=0.99720 C=0.00280
gnomAD - Exomes American Sub 34580 T=0.97568 C=0.02432
gnomAD - Exomes African Sub 16232 T=0.99027 C=0.00973
gnomAD - Exomes Ashkenazi Jewish Sub 10058 T=0.99105 C=0.00895
gnomAD - Exomes Other Sub 6126 T=0.9594 C=0.0406
gnomAD - Genomes Global Study-wide 140216 T=0.960411 C=0.039589
gnomAD - Genomes European Sub 75926 T=0.94171 C=0.05829
gnomAD - Genomes African Sub 42036 T=0.98987 C=0.01013
gnomAD - Genomes American Sub 13656 T=0.95723 C=0.04277
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9904 C=0.0096
gnomAD - Genomes East Asian Sub 3128 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2148 T=0.9614 C=0.0386
ExAC Global Study-wide 120648 T=0.960389 C=0.039611
ExAC Europe Sub 72744 T=0.94053 C=0.05947
ExAC Asian Sub 25132 T=0.99714 C=0.00286
ExAC American Sub 11540 T=0.97877 C=0.02123
ExAC African Sub 10338 T=0.98984 C=0.01016
ExAC Other Sub 894 T=0.965 C=0.035
The PAGE Study Global Study-wide 78694 T=0.97865 C=0.02135
The PAGE Study AfricanAmerican Sub 32512 T=0.98911 C=0.01089
The PAGE Study Mexican Sub 10810 T=0.96994 C=0.03006
The PAGE Study Asian Sub 8318 T=0.9995 C=0.0005
The PAGE Study PuertoRican Sub 7918 T=0.9446 C=0.0554
The PAGE Study NativeHawaiian Sub 4534 T=0.9852 C=0.0148
The PAGE Study Cuban Sub 4226 T=0.9534 C=0.0466
The PAGE Study Dominican Sub 3828 T=0.9673 C=0.0327
The PAGE Study CentralAmerican Sub 2450 T=0.9776 C=0.0224
The PAGE Study SouthAmerican Sub 1982 T=0.9682 C=0.0318
The PAGE Study NativeAmerican Sub 1260 T=0.9611 C=0.0389
The PAGE Study SouthAsian Sub 856 T=0.998 C=0.002
GO Exome Sequencing Project Global Study-wide 13006 T=0.96240 C=0.03760
GO Exome Sequencing Project European American Sub 8600 T=0.9483 C=0.0517
GO Exome Sequencing Project African American Sub 4406 T=0.9900 C=0.0100
1000Genomes Global Study-wide 5008 T=0.9798 C=0.0202
1000Genomes African Sub 1322 T=0.9970 C=0.0030
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9274 C=0.0726
1000Genomes South Asian Sub 978 T=0.998 C=0.002
1000Genomes American Sub 694 T=0.968 C=0.032
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9411 C=0.0589
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9393 C=0.0607
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9482 C=0.0518
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.931 C=0.069
Northern Sweden ACPOP Study-wide 600 T=0.927 C=0.073
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.951 C=0.049
FINRISK Finnish from FINRISK project Study-wide 304 T=0.891 C=0.109
The Danish reference pan genome Danish Study-wide 40 T=0.95 C=0.05
SGDP_PRJ Global Study-wide 10 T=0.5 C=0.5
Siberian Global Study-wide 2 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.6464628= NC_000001.11:g.6464628T>C
GRCh37.p13 chr 1 NC_000001.10:g.6524688= NC_000001.10:g.6524688T>C
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.60382= NG_007978.1:g.60382A>G
TNFRSF25 RefSeqGene NG_029910.1:g.6568= NG_029910.1:g.6568A>G
TNFRSF25 transcript variant 2 NM_003790.3:c.387= NM_003790.3:c.387A>G
TNFRSF25 transcript variant 2 NM_003790.2:c.387= NM_003790.2:c.387A>G
TNFRSF25 transcript variant 1 NM_148965.2:c.387= NM_148965.2:c.387A>G
TNFRSF25 transcript variant 1 NM_148965.1:c.387= NM_148965.1:c.387A>G
TNFRSF25 transcript variant 3 NM_148966.2:c.387= NM_148966.2:c.387A>G
TNFRSF25 transcript variant 3 NM_148966.1:c.387= NM_148966.1:c.387A>G
TNFRSF25 transcript variant 4 NM_148967.2:c.252= NM_148967.2:c.252A>G
TNFRSF25 transcript variant 4 NM_148967.1:c.252= NM_148967.1:c.252A>G
TNFRSF25 transcript variant 12 NM_001039664.2:c.387= NM_001039664.2:c.387A>G
TNFRSF25 transcript variant 12 NM_001039664.1:c.387= NM_001039664.1:c.387A>G
TNFRSF25 transcript variant 5 NM_148968.1:c.387= NM_148968.1:c.387A>G
TNFRSF25 transcript variant 6 NM_148969.1:c.387= NM_148969.1:c.387A>G
TNFRSF25 transcript variant 8 NM_148971.1:c.387= NM_148971.1:c.387A>G
TNFRSF25 transcript variant 9 NM_148972.1:c.387= NM_148972.1:c.387A>G
TNFRSF25 transcript variant 10 NM_148973.1:c.252= NM_148973.1:c.252A>G
TNFRSF25 transcript variant 11 NM_148974.1:c.252= NM_148974.1:c.252A>G
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Gln129= NP_003781.1:p.Gln129=
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Gln129= NP_683866.1:p.Gln129=
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Gln129= NP_683867.1:p.Gln129=
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Gln84= NP_683868.1:p.Gln84=
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Gln129= NP_001034753.1:p.Gln129=
TNFRSF25 transcript variant 7 NM_148970.1:c.160+812= NM_148970.1:c.160+812A>G
TNFRSF25 transcript variant 7 NM_148970.2:c.160+812= NM_148970.2:c.160+812A>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#.

57 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss4401753 May 29, 2002 (105)
2 LEE ss4438705 May 29, 2002 (105)
3 SEQUENOM ss24814366 Sep 20, 2004 (123)
4 CORNELL ss86257981 Mar 23, 2008 (129)
5 CANCER-GENOME ss86341805 Mar 23, 2008 (129)
6 1000GENOMES ss217314402 Jul 14, 2010 (132)
7 1000GENOMES ss217410499 Jul 14, 2010 (132)
8 1000GENOMES ss230414450 Jul 14, 2010 (132)
9 NHLBI-ESP ss341928673 May 09, 2011 (134)
10 ILLUMINA ss480080354 May 04, 2012 (137)
11 ILLUMINA ss482381087 May 04, 2012 (137)
12 1000GENOMES ss489717692 May 04, 2012 (137)
13 CLINSEQ_SNP ss491583250 May 04, 2012 (137)
14 ILLUMINA ss533527914 Sep 08, 2015 (146)
15 SSMP ss647552980 Apr 25, 2013 (138)
16 ILLUMINA ss779706770 Aug 21, 2014 (142)
17 ILLUMINA ss781141895 Aug 21, 2014 (142)
18 ILLUMINA ss835181020 Aug 21, 2014 (142)
19 EVA-GONL ss974820725 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1067415447 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067645527 Aug 21, 2014 (142)
22 1000GENOMES ss1289542645 Aug 21, 2014 (142)
23 EVA_GENOME_DK ss1573870590 Apr 01, 2015 (144)
24 EVA_FINRISK ss1584004193 Apr 01, 2015 (144)
25 EVA_DECODE ss1584178931 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1599475884 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1642469917 Apr 01, 2015 (144)
28 EVA_EXAC ss1685271976 Apr 01, 2015 (144)
29 EVA_MGP ss1710886359 Apr 01, 2015 (144)
30 ILLUMINA ss1958237405 Feb 12, 2016 (147)
31 JJLAB ss2019524942 Sep 14, 2016 (149)
32 USC_VALOUEV ss2147518263 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2159755149 Dec 20, 2016 (150)
34 TOPMED ss2321912280 Dec 20, 2016 (150)
35 GNOMAD ss2731072818 Nov 08, 2017 (151)
36 GNOMAD ss2746200466 Nov 08, 2017 (151)
37 GNOMAD ss2751216404 Nov 08, 2017 (151)
38 SWEGEN ss2986238941 Nov 08, 2017 (151)
39 ILLUMINA ss3021050293 Nov 08, 2017 (151)
40 TOPMED ss3067669965 Nov 08, 2017 (151)
41 CSHL ss3343301940 Nov 08, 2017 (151)
42 ILLUMINA ss3626017896 Oct 11, 2018 (152)
43 ILLUMINA ss3630511488 Oct 11, 2018 (152)
44 ILLUMINA ss3641569802 Oct 11, 2018 (152)
45 ILLUMINA ss3651373090 Oct 11, 2018 (152)
46 EGCUT_WGS ss3654338939 Jul 12, 2019 (153)
47 EVA_DECODE ss3686092726 Jul 12, 2019 (153)
48 ILLUMINA ss3724993024 Jul 12, 2019 (153)
49 ACPOP ss3726760589 Jul 12, 2019 (153)
50 PAGE_CC ss3770782679 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3798806748 Jul 12, 2019 (153)
52 EVA ss3823553113 Apr 25, 2020 (154)
53 EVA ss3825551842 Apr 25, 2020 (154)
54 EVA ss3826006678 Apr 25, 2020 (154)
55 SGDP_PRJ ss3848120392 Apr 25, 2020 (154)
56 EVA ss3986096306 Apr 25, 2021 (155)
57 TOPMED ss4438024156 Apr 25, 2021 (155)
58 1000Genomes NC_000001.10 - 6524688 Oct 11, 2018 (152)
59 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 6524688 Oct 11, 2018 (152)
60 Genetic variation in the Estonian population NC_000001.10 - 6524688 Oct 11, 2018 (152)
61 ExAC NC_000001.10 - 6524688 Oct 11, 2018 (152)
62 FINRISK NC_000001.10 - 6524688 Apr 25, 2020 (154)
63 The Danish reference pan genome NC_000001.10 - 6524688 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000001.11 - 6464628 Apr 25, 2021 (155)
65 gnomAD - Exomes NC_000001.10 - 6524688 Jul 12, 2019 (153)
66 GO Exome Sequencing Project NC_000001.10 - 6524688 Oct 11, 2018 (152)
67 Genome of the Netherlands Release 5 NC_000001.10 - 6524688 Apr 25, 2020 (154)
68 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 6524688 Apr 25, 2020 (154)
69 Northern Sweden NC_000001.10 - 6524688 Jul 12, 2019 (153)
70 The PAGE Study NC_000001.11 - 6464628 Jul 12, 2019 (153)
71 SGDP_PRJ NC_000001.10 - 6524688 Apr 25, 2020 (154)
72 Siberian NC_000001.10 - 6524688 Apr 25, 2020 (154)
73 TopMed NC_000001.11 - 6464628 Apr 25, 2021 (155)
74 UK 10K study - Twins NC_000001.10 - 6524688 Oct 11, 2018 (152)
75 ALFA NC_000001.11 - 6464628 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
ss217314402, ss217410499, ss482381087, ss491583250, ss1584178931 NC_000001.9:6447274:T:C NC_000001.11:6464627:T:C (self)
213476, 106259, 77187, 4448987, 654, 1377223, 87377, 11845, 46421, 3111, 45454, 137372, 34617, 106259, ss230414450, ss341928673, ss480080354, ss489717692, ss533527914, ss647552980, ss779706770, ss781141895, ss835181020, ss974820725, ss1067415447, ss1067645527, ss1289542645, ss1573870590, ss1584004193, ss1599475884, ss1642469917, ss1685271976, ss1710886359, ss1958237405, ss2019524942, ss2147518263, ss2321912280, ss2731072818, ss2746200466, ss2751216404, ss2986238941, ss3021050293, ss3343301940, ss3626017896, ss3630511488, ss3641569802, ss3651373090, ss3654338939, ss3726760589, ss3823553113, ss3825551842, ss3826006678, ss3848120392, ss3986096306 NC_000001.10:6524687:T:C NC_000001.11:6464627:T:C (self)
1469486, 4148, 1021493, 1630491, 4199086108, ss2159755149, ss3067669965, ss3686092726, ss3724993024, ss3770782679, ss3798806748, ss4438024156 NC_000001.11:6464627:T:C NC_000001.11:6464627:T:C (self)
ss4401753, ss4438705, ss24814366, ss86257981, ss86341805 NT_021937.19:2529419:T:C NC_000001.11:6464627: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 rs3170675

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