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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.

rs116290124

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:6465559 (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>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000310 (82/264690, TOPMED)
A=0.000342 (48/140206, GnomAD)
A=0.00006 (2/35430, ALFA) (+ 4 more)
A=0.00006 (1/16760, 8.3KJPN)
A=0.00038 (5/12988, GO-ESP)
A=0.0004 (2/5008, 1000G)
A=0.0007 (2/2920, KOREAN)
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.6465559G>A
GRCh38.p13 chr 1 NC_000001.11:g.6465559G>C
GRCh38.p13 chr 1 NC_000001.11:g.6465559G>T
GRCh37.p13 chr 1 NC_000001.10:g.6525619G>A
GRCh37.p13 chr 1 NC_000001.10:g.6525619G>C
GRCh37.p13 chr 1 NC_000001.10:g.6525619G>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.59451C>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.59451C>G
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.59451C>A
TNFRSF25 RefSeqGene NG_029910.1:g.5637C>T
TNFRSF25 RefSeqGene NG_029910.1:g.5637C>G
TNFRSF25 RefSeqGene NG_029910.1:g.5637C>A
Gene: TNFRSF25, TNF receptor superfamily member 25 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TNFRSF25 transcript variant 2 NM_003790.3:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 2 NM_003790.3:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Ala14Glu A (Ala) > E (Glu) Missense Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 12 NM_001039664.2:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Ala14Glu A (Ala) > E (Glu) Missense Variant
TNFRSF25 transcript variant 7 NM_148970.2:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 7 NM_148970.2:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 7 NM_148970.2:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Ala14Glu A (Ala) > E (Glu) Missense Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 1 NM_148965.2:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Ala14Glu A (Ala) > E (Glu) Missense Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 4 NM_148967.2:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Ala14Glu A (Ala) > E (Glu) Missense Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.41C>T A [GCG] > V [GTG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Ala14Val A (Ala) > V (Val) Missense Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.41C>G A [GCG] > G [GGG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Ala14Gly A (Ala) > G (Gly) Missense Variant
TNFRSF25 transcript variant 3 NM_148966.2:c.41C>A A [GCG] > E [GAG] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Ala14Glu A (Ala) > E (Glu) 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 35430 G=0.99994 A=0.00006
European Sub 26586 G=1.00000 A=0.00000
African Sub 2918 G=0.9997 A=0.0003
African Others Sub 114 G=1.000 A=0.000
African American Sub 2804 G=0.9996 A=0.0004
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 500 G=0.998 A=0.002
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 4588 G=1.0000 A=0.0000


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=0.999690 A=0.000310
gnomAD - Genomes Global Study-wide 140206 G=0.999658 A=0.000342
gnomAD - Genomes European Sub 75928 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42018 G=0.99891 A=0.00109
gnomAD - Genomes American Sub 13656 G=0.99985 A=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
GO Exome Sequencing Project Global Study-wide 12988 G=0.99962 A=0.00038
GO Exome Sequencing Project European American Sub 8596 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4392 G=0.9989 A=0.0011
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9993 A=0.0007
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= A C T
GRCh38.p13 chr 1 NC_000001.11:g.6465559= NC_000001.11:g.6465559G>A NC_000001.11:g.6465559G>C NC_000001.11:g.6465559G>T
GRCh37.p13 chr 1 NC_000001.10:g.6525619= NC_000001.10:g.6525619G>A NC_000001.10:g.6525619G>C NC_000001.10:g.6525619G>T
PLEKHG5 RefSeqGene (LRG_262) NG_007978.1:g.59451= NG_007978.1:g.59451C>T NG_007978.1:g.59451C>G NG_007978.1:g.59451C>A
TNFRSF25 RefSeqGene NG_029910.1:g.5637= NG_029910.1:g.5637C>T NG_029910.1:g.5637C>G NG_029910.1:g.5637C>A
TNFRSF25 transcript variant 2 NM_003790.3:c.41= NM_003790.3:c.41C>T NM_003790.3:c.41C>G NM_003790.3:c.41C>A
TNFRSF25 transcript variant 2 NM_003790.2:c.41= NM_003790.2:c.41C>T NM_003790.2:c.41C>G NM_003790.2:c.41C>A
TNFRSF25 transcript variant 1 NM_148965.2:c.41= NM_148965.2:c.41C>T NM_148965.2:c.41C>G NM_148965.2:c.41C>A
TNFRSF25 transcript variant 1 NM_148965.1:c.41= NM_148965.1:c.41C>T NM_148965.1:c.41C>G NM_148965.1:c.41C>A
TNFRSF25 transcript variant 3 NM_148966.2:c.41= NM_148966.2:c.41C>T NM_148966.2:c.41C>G NM_148966.2:c.41C>A
TNFRSF25 transcript variant 3 NM_148966.1:c.41= NM_148966.1:c.41C>T NM_148966.1:c.41C>G NM_148966.1:c.41C>A
TNFRSF25 transcript variant 4 NM_148967.2:c.41= NM_148967.2:c.41C>T NM_148967.2:c.41C>G NM_148967.2:c.41C>A
TNFRSF25 transcript variant 4 NM_148967.1:c.41= NM_148967.1:c.41C>T NM_148967.1:c.41C>G NM_148967.1:c.41C>A
TNFRSF25 transcript variant 7 NM_148970.2:c.41= NM_148970.2:c.41C>T NM_148970.2:c.41C>G NM_148970.2:c.41C>A
TNFRSF25 transcript variant 7 NM_148970.1:c.41= NM_148970.1:c.41C>T NM_148970.1:c.41C>G NM_148970.1:c.41C>A
TNFRSF25 transcript variant 12 NM_001039664.2:c.41= NM_001039664.2:c.41C>T NM_001039664.2:c.41C>G NM_001039664.2:c.41C>A
TNFRSF25 transcript variant 12 NM_001039664.1:c.41= NM_001039664.1:c.41C>T NM_001039664.1:c.41C>G NM_001039664.1:c.41C>A
TNFRSF25 transcript variant 5 NM_148968.1:c.41= NM_148968.1:c.41C>T NM_148968.1:c.41C>G NM_148968.1:c.41C>A
TNFRSF25 transcript variant 6 NM_148969.1:c.41= NM_148969.1:c.41C>T NM_148969.1:c.41C>G NM_148969.1:c.41C>A
TNFRSF25 transcript variant 8 NM_148971.1:c.41= NM_148971.1:c.41C>T NM_148971.1:c.41C>G NM_148971.1:c.41C>A
TNFRSF25 transcript variant 9 NM_148972.1:c.41= NM_148972.1:c.41C>T NM_148972.1:c.41C>G NM_148972.1:c.41C>A
TNFRSF25 transcript variant 10 NM_148973.1:c.41= NM_148973.1:c.41C>T NM_148973.1:c.41C>G NM_148973.1:c.41C>A
TNFRSF25 transcript variant 11 NM_148974.1:c.41= NM_148974.1:c.41C>T NM_148974.1:c.41C>G NM_148974.1:c.41C>A
tumor necrosis factor receptor superfamily member 25 isoform 2 precursor NP_003781.1:p.Ala14= NP_003781.1:p.Ala14Val NP_003781.1:p.Ala14Gly NP_003781.1:p.Ala14Glu
tumor necrosis factor receptor superfamily member 25 isoform 1 precursor NP_683866.1:p.Ala14= NP_683866.1:p.Ala14Val NP_683866.1:p.Ala14Gly NP_683866.1:p.Ala14Glu
tumor necrosis factor receptor superfamily member 25 isoform 3 precursor NP_683867.1:p.Ala14= NP_683867.1:p.Ala14Val NP_683867.1:p.Ala14Gly NP_683867.1:p.Ala14Glu
tumor necrosis factor receptor superfamily member 25 isoform 4 precursor NP_683868.1:p.Ala14= NP_683868.1:p.Ala14Val NP_683868.1:p.Ala14Gly NP_683868.1:p.Ala14Glu
tumor necrosis factor receptor superfamily member 25 isoform 7 precursor NP_683871.1:p.Ala14= NP_683871.1:p.Ala14Val NP_683871.1:p.Ala14Gly NP_683871.1:p.Ala14Glu
tumor necrosis factor receptor superfamily member 25 isoform 12 precursor NP_001034753.1:p.Ala14= NP_001034753.1:p.Ala14Val NP_001034753.1:p.Ala14Gly NP_001034753.1:p.Ala14Glu
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#.

19 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217405850 Jul 14, 2010 (132)
2 NHLBI-ESP ss341928696 May 09, 2011 (134)
3 1000GENOMES ss488649807 May 04, 2012 (137)
4 EXOME_CHIP ss491285330 May 04, 2012 (137)
5 1000GENOMES ss1289542674 Aug 21, 2014 (142)
6 EVA_EXAC ss1685272066 Apr 01, 2015 (144)
7 EVA_EXAC ss1685272067 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2159755207 Dec 20, 2016 (150)
9 TOPMED ss2321912330 Dec 20, 2016 (150)
10 GNOMAD ss2731072957 Nov 08, 2017 (151)
11 GNOMAD ss2746200500 Nov 08, 2017 (151)
12 GNOMAD ss2751216473 Nov 08, 2017 (151)
13 TOPMED ss3067670131 Nov 08, 2017 (151)
14 EVA_DECODE ss3686092736 Jul 12, 2019 (153)
15 EVA ss3823553133 Apr 25, 2020 (154)
16 KRGDB ss3892987917 Apr 25, 2020 (154)
17 EVA ss3986096316 Apr 25, 2021 (155)
18 TOPMED ss4438024390 Apr 25, 2021 (155)
19 TOMMO_GENOMICS ss5142303853 Apr 25, 2021 (155)
20 1000Genomes NC_000001.10 - 6525619 Oct 11, 2018 (152)
21 ExAC

Submission ignored due to conflicting rows:
Row 4449083 (NC_000001.10:6525618:G:G 99705/99722, NC_000001.10:6525618:G:A 17/99722)
Row 4449084 (NC_000001.10:6525618:G:G 99721/99722, NC_000001.10:6525618:G:C 1/99722)

- Oct 11, 2018 (152)
22 ExAC

Submission ignored due to conflicting rows:
Row 4449083 (NC_000001.10:6525618:G:G 99705/99722, NC_000001.10:6525618:G:A 17/99722)
Row 4449084 (NC_000001.10:6525618:G:G 99721/99722, NC_000001.10:6525618:G:C 1/99722)

- Oct 11, 2018 (152)
23 gnomAD - Genomes NC_000001.11 - 6465559 Apr 25, 2021 (155)
24 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 87532 (NC_000001.10:6525618:G:G 244078/244104, NC_000001.10:6525618:G:A 26/244104)
Row 87533 (NC_000001.10:6525618:G:G 244102/244104, NC_000001.10:6525618:G:C 2/244104)

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

Submission ignored due to conflicting rows:
Row 87532 (NC_000001.10:6525618:G:G 244078/244104, NC_000001.10:6525618:G:A 26/244104)
Row 87533 (NC_000001.10:6525618:G:G 244102/244104, NC_000001.10:6525618:G:C 2/244104)

- Jul 12, 2019 (153)
26 GO Exome Sequencing Project NC_000001.10 - 6525619 Oct 11, 2018 (152)
27 KOREAN population from KRGDB NC_000001.10 - 6525619 Apr 25, 2020 (154)
28 8.3KJPN NC_000001.10 - 6525619 Apr 25, 2021 (155)
29 TopMed NC_000001.11 - 6465559 Apr 25, 2021 (155)
30 ALFA NC_000001.11 - 6465559 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
ss217405850 NC_000001.9:6448205:G:A NC_000001.11:6465558:G:A (self)
213505, 11865, 165311, 273160, ss341928696, ss488649807, ss491285330, ss1289542674, ss1685272066, ss2321912330, ss2731072957, ss2746200500, ss2751216473, ss3823553133, ss3892987917, ss3986096316, ss5142303853 NC_000001.10:6525618:G:A NC_000001.11:6465558:G:A (self)
1469656, 1021639, 1630725, 8264865232, ss2159755207, ss3067670131, ss4438024390 NC_000001.11:6465558:G:A NC_000001.11:6465558:G:A (self)
ss1685272067, ss2731072957 NC_000001.10:6525618:G:C NC_000001.11:6465558:G:C (self)
ss3686092736 NC_000001.11:6465558:G:T NC_000001.11:6465558:G: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 rs116290124

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