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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs5746027

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:12193017 (GRCh38.p14) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000359 (95/264690, TOPMED)
A=0.000127 (32/251300, GnomAD_exome)
A=0.000435 (61/140244, GnomAD) (+ 6 more)
A=0.000149 (18/120736, ExAC)
A=0.00009 (2/21894, ALFA)
A=0.00100 (13/13006, GO-ESP)
A=0.0003 (2/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
A=0.007 (4/594, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TNFRSF1B : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 38256 G=0.99979 A=0.00021
European Sub 25928 G=0.99996 A=0.00004
African Sub 8874 G=0.9992 A=0.0008
African Others Sub 328 G=1.000 A=0.000
African American Sub 8546 G=0.9992 A=0.0008
Asian Sub 116 G=1.000 A=0.000
East Asian Sub 88 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 154 G=1.000 A=0.000
Latin American 2 Sub 616 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 2470 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=0.999641 A=0.000359
gnomAD - Exomes Global Study-wide 251300 G=0.999873 A=0.000127
gnomAD - Exomes European Sub 135256 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49008 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34586 G=0.99988 A=0.00012
gnomAD - Exomes African Sub 16238 G=0.99828 A=0.00172
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6134 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140244 G=0.999565 A=0.000435
gnomAD - Genomes European Sub 75946 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42032 G=0.99857 A=0.00143
gnomAD - Genomes American Sub 13662 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 G=1.0000 A=0.0000
ExAC Global Study-wide 120736 G=0.999851 A=0.000149
ExAC Europe Sub 72874 G=1.00000 A=0.00000
ExAC Asian Sub 25124 G=1.00000 A=0.00000
ExAC American Sub 11526 G=0.99991 A=0.00009
ExAC African Sub 10320 G=0.99835 A=0.00165
ExAC Other Sub 892 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 21894 G=0.99991 A=0.00009
Allele Frequency Aggregator European Sub 15838 G=0.99994 A=0.00006
Allele Frequency Aggregator African Sub 4036 G=0.9998 A=0.0002
Allele Frequency Aggregator Other Sub 1036 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 616 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 116 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.99900 A=0.00100
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9970 A=0.0030
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
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
HapMap Global Study-wide 594 G=0.993 A=0.007
HapMap African Sub 294 G=0.990 A=0.010
HapMap American Sub 214 G=0.995 A=0.005
HapMap Asian Sub 86 G=1.00 A=0.00
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.p14 chr 1 NC_000001.11:g.12193017G>A
GRCh37.p13 chr 1 NC_000001.10:g.12253074G>A
TNFRSF1B RefSeqGene NG_029791.1:g.31015G>A
Gene: TNFRSF1B, TNF receptor superfamily member 1B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TNFRSF1B transcript NM_001066.3:c.706G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B precursor NP_001057.1:p.Ala236Thr A (Ala) > T (Thr) Missense Variant
TNFRSF1B transcript variant X1 XM_011542060.3:c.706G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B isoform X1 XP_011540362.1:p.Ala236Thr A (Ala) > T (Thr) Missense Variant
TNFRSF1B transcript variant X2 XM_047429422.1:c.706G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B isoform X2 XP_047285378.1:p.Ala236Thr A (Ala) > T (Thr) Missense Variant
TNFRSF1B transcript variant X3 XM_047429423.1:c.685G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B isoform X3 XP_047285379.1:p.Ala229Thr A (Ala) > T (Thr) Missense Variant
TNFRSF1B transcript variant X4 XM_011542063.3:c.706G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B isoform X4 XP_011540365.1:p.Ala236Thr A (Ala) > T (Thr) Missense Variant
TNFRSF1B transcript variant X5 XM_047429424.1:c.553G>A A [GCT] > T [ACT] Coding Sequence Variant
tumor necrosis factor receptor superfamily member 1B isoform X5 XP_047285380.1:p.Ala185Thr A (Ala) > T (Thr) 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
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
GRCh38.p14 chr 1 NC_000001.11:g.12193017= NC_000001.11:g.12193017G>A
GRCh37.p13 chr 1 NC_000001.10:g.12253074= NC_000001.10:g.12253074G>A
TNFRSF1B RefSeqGene NG_029791.1:g.31015= NG_029791.1:g.31015G>A
TNFRSF1B transcript NM_001066.3:c.706= NM_001066.3:c.706G>A
TNFRSF1B transcript NM_001066.2:c.706= NM_001066.2:c.706G>A
TNFRSF1B transcript variant X1 XM_011542060.3:c.706= XM_011542060.3:c.706G>A
TNFRSF1B transcript variant X2 XM_011542060.2:c.706= XM_011542060.2:c.706G>A
TNFRSF1B transcript variant X1 XM_011542060.1:c.706= XM_011542060.1:c.706G>A
TNFRSF1B transcript variant X4 XM_011542063.3:c.706= XM_011542063.3:c.706G>A
TNFRSF1B transcript variant X3 XM_011542063.2:c.706= XM_011542063.2:c.706G>A
TNFRSF1B transcript variant X4 XM_011542063.1:c.706= XM_011542063.1:c.706G>A
TNFRSF1B transcript variant X5 XM_047429424.1:c.553= XM_047429424.1:c.553G>A
TNFRSF1B transcript variant X3 XM_047429423.1:c.685= XM_047429423.1:c.685G>A
TNFRSF1B transcript variant X2 XM_047429422.1:c.706= XM_047429422.1:c.706G>A
tumor necrosis factor receptor superfamily member 1B precursor NP_001057.1:p.Ala236= NP_001057.1:p.Ala236Thr
tumor necrosis factor receptor superfamily member 1B isoform X1 XP_011540362.1:p.Ala236= XP_011540362.1:p.Ala236Thr
tumor necrosis factor receptor superfamily member 1B isoform X4 XP_011540365.1:p.Ala236= XP_011540365.1:p.Ala236Thr
tumor necrosis factor receptor superfamily member 1B isoform X5 XP_047285380.1:p.Ala185= XP_047285380.1:p.Ala185Thr
tumor necrosis factor receptor superfamily member 1B isoform X3 XP_047285379.1:p.Ala229= XP_047285379.1:p.Ala229Thr
tumor necrosis factor receptor superfamily member 1B isoform X2 XP_047285378.1:p.Ala236= XP_047285378.1:p.Ala236Thr
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#.

30 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss7990729 Apr 21, 2003 (114)
2 ILLUMINA ss74910587 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119498167 Dec 01, 2009 (131)
4 ILLUMINA ss173926547 Jul 04, 2010 (132)
5 ILLUMINA ss244303502 Jul 04, 2010 (132)
6 1000GENOMES ss328418557 May 09, 2011 (134)
7 NHLBI-ESP ss341934004 May 09, 2011 (134)
8 1000GENOMES ss489721551 May 04, 2012 (137)
9 EXOME_CHIP ss491286400 May 04, 2012 (137)
10 ILLUMINA ss537313616 Sep 08, 2015 (146)
11 1000GENOMES ss1289714037 Aug 21, 2014 (142)
12 EVA_EXAC ss1685309328 Apr 01, 2015 (144)
13 HUMAN_LONGEVITY ss2160112171 Dec 20, 2016 (150)
14 GNOMAD ss2731129164 Nov 08, 2017 (151)
15 GNOMAD ss2746218120 Nov 08, 2017 (151)
16 GNOMAD ss2751709569 Nov 08, 2017 (151)
17 AFFY ss2984845576 Nov 08, 2017 (151)
18 ILLUMINA ss3626028000 Oct 11, 2018 (152)
19 ILLUMINA ss3637737901 Oct 11, 2018 (152)
20 ILLUMINA ss3642751649 Oct 11, 2018 (152)
21 ILLUMINA ss3653619221 Oct 11, 2018 (152)
22 EVA ss3823561443 Apr 25, 2020 (154)
23 EVA ss4016893786 Apr 25, 2021 (155)
24 TOPMED ss4439478637 Apr 25, 2021 (155)
25 1000G_HIGH_COVERAGE ss5241204975 Oct 12, 2022 (156)
26 EVA ss5316801525 Oct 12, 2022 (156)
27 HUGCELL_USP ss5442406121 Oct 12, 2022 (156)
28 1000G_HIGH_COVERAGE ss5512975194 Oct 12, 2022 (156)
29 EVA ss5907075843 Oct 12, 2022 (156)
30 EVA ss5936767768 Oct 12, 2022 (156)
31 1000Genomes NC_000001.10 - 12253074 Oct 11, 2018 (152)
32 1000Genomes_30x NC_000001.11 - 12193017 Oct 12, 2022 (156)
33 ExAC NC_000001.10 - 12253074 Oct 11, 2018 (152)
34 gnomAD - Genomes NC_000001.11 - 12193017 Apr 25, 2021 (155)
35 gnomAD - Exomes NC_000001.10 - 12253074 Jul 12, 2019 (153)
36 GO Exome Sequencing Project NC_000001.10 - 12253074 Oct 11, 2018 (152)
37 HapMap NC_000001.11 - 12193017 Apr 25, 2020 (154)
38 TopMed NC_000001.11 - 12193017 Apr 25, 2021 (155)
39 ALFA NC_000001.11 - 12193017 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
ss3642751649 NC_000001.9:12175660:G:A NC_000001.11:12193016:G:A (self)
391218, 4489087, 145748, 20168, ss328418557, ss341934004, ss489721551, ss491286400, ss537313616, ss1289714037, ss1685309328, ss2731129164, ss2746218120, ss2751709569, ss2984845576, ss3626028000, ss3637737901, ss3653619221, ss3823561443, ss4016893786, ss5316801525, ss5936767768 NC_000001.10:12253073:G:A NC_000001.11:12193016:G:A (self)
501129, 2718260, 14687, 3084972, 9154453260, ss2160112171, ss4439478637, ss5241204975, ss5442406121, ss5512975194, ss5907075843 NC_000001.11:12193016:G:A NC_000001.11:12193016:G:A (self)
ss7990729, ss74910587, ss119498167, ss173926547, ss244303502 NT_021937.19:8257805:G:A NC_000001.11:12193016:G:A (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 rs5746027

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.post761+d5e8e07