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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 Aliases 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.

rs4848978

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr2:112058470 (GRCh38.p12) 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
T=0.26291 (33013/125568, TOPMED)
T=0.2517 (19748/78466, PAGE_STUDY)
T=0.2950 (9249/31356, GnomAD) (+ 6 more)
T=0.253 (1265/5008, 1000G)
T=0.382 (1713/4480, Estonian)
T=0.286 (1101/3854, ALSPAC)
T=0.285 (1057/3708, TWINSUK)
T=0.30 (179/600, NorthernSweden)
T=0.12 (25/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEM87B : Intron 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.p12 chr 2 NC_000002.12:g.112058470T>A
GRCh38.p12 chr 2 NC_000002.12:g.112058470T>C
GRCh37.p13 chr 2 NC_000002.11:g.112816047T>A
GRCh37.p13 chr 2 NC_000002.11:g.112816047T>C
TMEM87B RefSeqGene NG_051358.1:g.8248T>A
TMEM87B RefSeqGene NG_051358.1:g.8248T>C
Gene: TMEM87B, transmembrane protein 87B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM87B transcript variant 2 NM_001329914.2:c. N/A Intron Variant
TMEM87B transcript variant 1 NM_032824.3:c. N/A Intron Variant
TMEM87B transcript variant X1 XM_005263827.2:c. N/A Intron Variant
TMEM87B transcript variant X2 XM_017005121.1:c. N/A Intron Variant
TMEM87B transcript variant X3 XR_923049.2:n. N/A Intron 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

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 125568 T=0.26291 C=0.73709
The PAGE Study Global Study-wide 78466 T=0.2517 C=0.7483
The PAGE Study AfricanAmerican Sub 32418 T=0.2327 C=0.7673
The PAGE Study Mexican Sub 10780 T=0.4086 C=0.5914
The PAGE Study Asian Sub 8298 T=0.105 C=0.895
The PAGE Study PuertoRican Sub 7890 T=0.251 C=0.749
The PAGE Study NativeHawaiian Sub 4512 T=0.157 C=0.843
The PAGE Study Cuban Sub 4218 T=0.250 C=0.750
The PAGE Study Dominican Sub 3820 T=0.237 C=0.763
The PAGE Study CentralAmerican Sub 2440 T=0.367 C=0.633
The PAGE Study SouthAmerican Sub 1976 T=0.359 C=0.641
The PAGE Study NativeAmerican Sub 1258 T=0.327 C=0.673
The PAGE Study SouthAsian Sub 856 T=0.31 C=0.69
gnomAD - Genomes Global Study-wide 31356 T=0.2950 C=0.7050
gnomAD - Genomes European Sub 18878 T=0.3315 C=0.6685
gnomAD - Genomes African Sub 8700 T=0.238 C=0.762
gnomAD - Genomes East Asian Sub 1558 T=0.089 C=0.911
gnomAD - Genomes Other Sub 1086 T=0.342 C=0.658
gnomAD - Genomes American Sub 844 T=0.38 C=0.62
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.30 C=0.70
1000Genomes Global Study-wide 5008 T=0.253 C=0.747
1000Genomes African Sub 1322 T=0.204 C=0.796
1000Genomes East Asian Sub 1008 T=0.085 C=0.915
1000Genomes Europe Sub 1006 T=0.318 C=0.682
1000Genomes South Asian Sub 978 T=0.36 C=0.64
1000Genomes American Sub 694 T=0.35 C=0.65
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.382 C=0.618
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.286 C=0.714
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.285 C=0.715
Northern Sweden ACPOP Study-wide 600 T=0.30 C=0.70
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.12 C=0.88
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 Note
GRCh38.p12 chr 2 NC_000002.12:g.11...

NC_000002.12:g.112058470=

NC_000002.12:g.11...

NC_000002.12:g.112058470T>A

NC_000002.12:g.11...

NC_000002.12:g.112058470T>C

GRCh37.p13 chr 2 NC_000002.11:g.11...

NC_000002.11:g.112816047=

NC_000002.11:g.11...

NC_000002.11:g.112816047T>A

NC_000002.11:g.11...

NC_000002.11:g.112816047T>C

TMEM87B RefSeqGene NG_051358.1:g.8248= NG_051358.1:g.824...

NG_051358.1:g.8248T>A

NG_051358.1:g.824...

NG_051358.1:g.8248T>C

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#.

111 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6699058 Feb 20, 2003 (111)
2 SSAHASNP ss21673717 Apr 05, 2004 (121)
3 ABI ss44364778 Mar 14, 2006 (126)
4 ILLUMINA ss65793924 Oct 13, 2006 (127)
5 ILLUMINA ss66588606 Nov 29, 2006 (127)
6 ILLUMINA ss70830220 May 25, 2008 (130)
7 ILLUMINA ss71412790 May 16, 2007 (127)
8 ILLUMINA ss74935119 Dec 07, 2007 (129)
9 ILLUMINA ss79198759 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss91297073 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96417787 Feb 05, 2009 (130)
12 BGI ss106110299 Feb 05, 2009 (130)
13 1000GENOMES ss109782473 Jan 24, 2009 (130)
14 1000GENOMES ss110744075 Jan 25, 2009 (130)
15 ILLUMINA-UK ss117829563 Feb 14, 2009 (130)
16 ILLUMINA ss122408622 Dec 01, 2009 (131)
17 ENSEMBL ss132808692 Dec 01, 2009 (131)
18 ENSEMBL ss138506547 Dec 01, 2009 (131)
19 ILLUMINA ss154322841 Dec 01, 2009 (131)
20 GMI ss157504848 Dec 01, 2009 (131)
21 ILLUMINA ss159499450 Dec 01, 2009 (131)
22 ILLUMINA ss160719379 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss163943279 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss164990924 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss167023813 Jul 04, 2010 (132)
26 ILLUMINA ss171946352 Jul 04, 2010 (132)
27 ILLUMINA ss173843057 Jul 04, 2010 (132)
28 BUSHMAN ss200885174 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss205624184 Jul 04, 2010 (132)
30 1000GENOMES ss219436597 Jul 14, 2010 (132)
31 1000GENOMES ss231309024 Jul 14, 2010 (132)
32 1000GENOMES ss238830848 Jul 15, 2010 (132)
33 BL ss253372193 May 09, 2011 (134)
34 GMI ss276622506 May 04, 2012 (137)
35 GMI ss284411657 Apr 25, 2013 (138)
36 PJP ss292341670 May 09, 2011 (134)
37 ILLUMINA ss481072556 May 04, 2012 (137)
38 ILLUMINA ss481094480 May 04, 2012 (137)
39 ILLUMINA ss482088053 Sep 08, 2015 (146)
40 ILLUMINA ss485331408 May 04, 2012 (137)
41 ILLUMINA ss537283508 Sep 08, 2015 (146)
42 TISHKOFF ss555792197 Apr 25, 2013 (138)
43 SSMP ss649411606 Apr 25, 2013 (138)
44 ILLUMINA ss778921928 Sep 08, 2015 (146)
45 ILLUMINA ss783111475 Sep 08, 2015 (146)
46 ILLUMINA ss784068452 Sep 08, 2015 (146)
47 ILLUMINA ss825529277 Apr 01, 2015 (144)
48 ILLUMINA ss832370154 Sep 08, 2015 (146)
49 ILLUMINA ss833010813 Jul 13, 2019 (153)
50 ILLUMINA ss834383373 Sep 08, 2015 (146)
51 EVA-GONL ss977219752 Aug 21, 2014 (142)
52 JMKIDD_LAB ss1069392286 Aug 21, 2014 (142)
53 1000GENOMES ss1298776547 Aug 21, 2014 (142)
54 DDI ss1428692182 Apr 01, 2015 (144)
55 EVA_GENOME_DK ss1579030362 Apr 01, 2015 (144)
56 EVA_DECODE ss1586643576 Apr 01, 2015 (144)
57 EVA_UK10K_ALSPAC ss1604287235 Apr 01, 2015 (144)
58 EVA_UK10K_TWINSUK ss1647281268 Apr 01, 2015 (144)
59 EVA_SVP ss1712481178 Apr 01, 2015 (144)
60 ILLUMINA ss1752305323 Sep 08, 2015 (146)
61 HAMMER_LAB ss1797289897 Sep 08, 2015 (146)
62 WEILL_CORNELL_DGM ss1920465807 Feb 12, 2016 (147)
63 ILLUMINA ss1946049356 Feb 12, 2016 (147)
64 ILLUMINA ss1958448693 Feb 12, 2016 (147)
65 GENOMED ss1968855383 Jul 19, 2016 (147)
66 JJLAB ss2020762261 Sep 14, 2016 (149)
67 USC_VALOUEV ss2148818114 Dec 20, 2016 (150)
68 HUMAN_LONGEVITY ss2233257406 Dec 20, 2016 (150)
69 TOPMED ss2399485933 Dec 20, 2016 (150)
70 SYSTEMSBIOZJU ss2624887095 Nov 08, 2017 (151)
71 ILLUMINA ss2633657930 Nov 08, 2017 (151)
72 GRF ss2703427737 Nov 08, 2017 (151)
73 ILLUMINA ss2710909113 Nov 08, 2017 (151)
74 GNOMAD ss2778072742 Nov 08, 2017 (151)
75 SWEGEN ss2990189204 Nov 08, 2017 (151)
76 ILLUMINA ss3022004945 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3024142719 Nov 08, 2017 (151)
78 TOPMED ss3319370302 Nov 08, 2017 (151)
79 TOPMED ss3319370303 Nov 08, 2017 (151)
80 CSHL ss3344409793 Nov 08, 2017 (151)
81 ILLUMINA ss3625763198 Oct 11, 2018 (152)
82 ILLUMINA ss3628139826 Oct 11, 2018 (152)
83 ILLUMINA ss3631622385 Oct 11, 2018 (152)
84 ILLUMINA ss3633212344 Oct 11, 2018 (152)
85 ILLUMINA ss3633924560 Oct 11, 2018 (152)
86 ILLUMINA ss3634782430 Oct 11, 2018 (152)
87 ILLUMINA ss3635610549 Oct 11, 2018 (152)
88 ILLUMINA ss3636470599 Oct 11, 2018 (152)
89 ILLUMINA ss3637362472 Oct 11, 2018 (152)
90 ILLUMINA ss3638280529 Oct 11, 2018 (152)
91 ILLUMINA ss3639584767 Oct 11, 2018 (152)
92 ILLUMINA ss3640489731 Oct 11, 2018 (152)
93 ILLUMINA ss3641111803 Oct 11, 2018 (152)
94 ILLUMINA ss3641407760 Oct 11, 2018 (152)
95 ILLUMINA ss3643248549 Oct 11, 2018 (152)
96 ILLUMINA ss3644752054 Oct 11, 2018 (152)
97 URBANLAB ss3647112897 Oct 11, 2018 (152)
98 ILLUMINA ss3652444804 Oct 11, 2018 (152)
99 EGCUT_WGS ss3658067848 Jul 13, 2019 (153)
100 EVA_DECODE ss3704632119 Jul 13, 2019 (153)
101 ILLUMINA ss3725814137 Jul 13, 2019 (153)
102 ACPOP ss3728750963 Jul 13, 2019 (153)
103 ILLUMINA ss3744180842 Jul 13, 2019 (153)
104 ILLUMINA ss3745082308 Jul 13, 2019 (153)
105 EVA ss3757216699 Jul 13, 2019 (153)
106 PAGE_CC ss3770941688 Jul 13, 2019 (153)
107 ILLUMINA ss3772579027 Jul 13, 2019 (153)
108 PACBIO ss3783958548 Jul 13, 2019 (153)
109 PACBIO ss3789527952 Jul 13, 2019 (153)
110 PACBIO ss3794400759 Jul 13, 2019 (153)
111 KHV_HUMAN_GENOMES ss3801582794 Jul 13, 2019 (153)
112 1000Genomes NC_000002.11 - 112816047 Oct 11, 2018 (152)
113 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 112816047 Oct 11, 2018 (152)
114 Genetic variation in the Estonian population NC_000002.11 - 112816047 Oct 11, 2018 (152)
115 gnomAD - Genomes NC_000002.11 - 112816047 Jul 13, 2019 (153)
116 Northern Sweden NC_000002.11 - 112816047 Jul 13, 2019 (153)
117 The PAGE Study NC_000002.12 - 112058470 Jul 13, 2019 (153)
118 TopMed NC_000002.12 - 112058470 Oct 11, 2018 (152)
119 UK 10K study - Twins NC_000002.11 - 112816047 Oct 11, 2018 (152)
120 A Vietnamese Genetic Variation Database NC_000002.11 - 112816047 Jul 13, 2019 (153)
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)
rs59989170 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3319370302 NC_000002.12:112058469:T:A NC_000002.12:112058469:T:A (self)
ss3639584767 NC_000002.9:112532277:T:C NC_000002.12:112058469:T:C (self)
ss91297073, ss109782473, ss110744075, ss117829563, ss163943279, ss164990924, ss167023813, ss200885174, ss205624184, ss253372193, ss276622506, ss284411657, ss292341670, ss481072556, ss825529277, ss1586643576, ss1712481178, ss3643248549 NC_000002.10:112532517:T:C NC_000002.12:112058469:T:C (self)
9773611, 5392360, 3806096, 26705788, 2035828, 5392360, 1169599, ss219436597, ss231309024, ss238830848, ss481094480, ss482088053, ss485331408, ss537283508, ss555792197, ss649411606, ss778921928, ss783111475, ss784068452, ss832370154, ss833010813, ss834383373, ss977219752, ss1069392286, ss1298776547, ss1428692182, ss1579030362, ss1604287235, ss1647281268, ss1752305323, ss1797289897, ss1920465807, ss1946049356, ss1958448693, ss1968855383, ss2020762261, ss2148818114, ss2399485933, ss2624887095, ss2633657930, ss2703427737, ss2710909113, ss2778072742, ss2990189204, ss3022004945, ss3344409793, ss3625763198, ss3628139826, ss3631622385, ss3633212344, ss3633924560, ss3634782430, ss3635610549, ss3636470599, ss3637362472, ss3638280529, ss3640489731, ss3641111803, ss3641407760, ss3644752054, ss3652444804, ss3658067848, ss3728750963, ss3744180842, ss3745082308, ss3757216699, ss3772579027, ss3783958548, ss3789527952, ss3794400759 NC_000002.11:112816046:T:C NC_000002.12:112058469:T:C (self)
163157, 201559107, ss2233257406, ss3024142719, ss3319370303, ss3647112897, ss3704632119, ss3725814137, ss3770941688, ss3801582794 NC_000002.12:112058469:T:C NC_000002.12:112058469:T:C (self)
ss21673717 NT_022135.13:1523789:T:C NC_000002.12:112058469:T:C (self)
ss6699058, ss44364778, ss65793924, ss66588606, ss70830220, ss71412790, ss74935119, ss79198759, ss96417787, ss106110299, ss122408622, ss132808692, ss138506547, ss154322841, ss157504848, ss159499450, ss160719379, ss171946352, ss173843057 NT_022135.16:2564709:T:C NC_000002.12:112058469: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 rs4848978

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.post308+0fe9b3b