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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.

rs6800

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:156292862 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.234999 (62202/264690, TOPMED)
C=0.241392 (33790/139980, GnomAD)
C=0.27015 (7716/28562, ALFA) (+ 16 more)
C=0.21715 (3639/16758, 8.3KJPN)
C=0.2065 (1034/5008, 1000G)
C=0.3411 (1528/4480, Estonian)
C=0.2854 (1100/3854, ALSPAC)
C=0.2778 (1030/3708, TWINSUK)
C=0.2329 (681/2924, KOREAN)
C=0.1741 (329/1890, HapMap)
C=0.2718 (498/1832, Korea1K)
C=0.299 (298/998, GoNL)
C=0.370 (222/600, NorthernSweden)
C=0.189 (101/534, MGP)
A=0.428 (101/236, SGDP_PRJ)
C=0.227 (49/216, Qatari)
C=0.238 (51/214, Vietnamese)
C=0.28 (11/40, GENOME_DK)
A=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GLMP : Non Coding Transcript Variant
SMG5 : 2KB Upstream Variant
TMEM79 : 500B Downstream 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.156292862A>C
GRCh37.p13 chr 1 NC_000001.10:g.156262653A>C
Gene: GLMP, glycosylated lysosomal membrane protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GLMP transcript variant 1 NM_144580.3:c.*182= N/A 3 Prime UTR Variant
GLMP transcript variant 5 NM_001256609.2:c.*182= N/A 3 Prime UTR Variant
GLMP transcript variant 4 NM_001256608.2:c.*150= N/A 3 Prime UTR Variant
GLMP transcript variant 3 NM_001256605.2:c.*182= N/A 3 Prime UTR Variant
GLMP transcript variant 2 NM_001256604.2:c.*182= N/A 3 Prime UTR Variant
GLMP transcript variant X2 XM_011509117.3:c.*182= N/A 3 Prime UTR Variant
GLMP transcript variant X1 XR_426762.3:n.1283T>G N/A Non Coding Transcript Variant
Gene: SMG5, SMG5 nonsense mediated mRNA decay factor (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SMG5 transcript variant 5 NM_001323617.2:c. N/A Upstream Transcript Variant
SMG5 transcript variant 2 NM_001323614.2:c. N/A N/A
SMG5 transcript variant 3 NM_001323615.2:c. N/A N/A
SMG5 transcript variant 4 NM_001323616.2:c. N/A N/A
SMG5 transcript variant 1 NM_015327.3:c. N/A N/A
Gene: TMEM79, transmembrane protein 79 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TMEM79 transcript variant 1 NM_032323.3:c. N/A Downstream Transcript Variant
TMEM79 transcript variant 2 NR_026678.2:n. N/A Downstream Transcript 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 28562 A=0.72985 C=0.27015
European Sub 22602 A=0.70171 C=0.29829
African Sub 4090 A=0.8773 C=0.1227
African Others Sub 148 A=0.905 C=0.095
African American Sub 3942 A=0.8762 C=0.1238
Asian Sub 120 A=0.767 C=0.233
East Asian Sub 94 A=0.83 C=0.17
Other Asian Sub 26 A=0.54 C=0.46
Latin American 1 Sub 160 A=0.725 C=0.275
Latin American 2 Sub 664 A=0.706 C=0.294
South Asian Sub 98 A=0.82 C=0.18
Other Sub 828 A=0.774 C=0.226


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 A=0.765001 C=0.234999
gnomAD - Genomes Global Study-wide 139980 A=0.758608 C=0.241392
gnomAD - Genomes European Sub 75794 A=0.70429 C=0.29571
gnomAD - Genomes African Sub 41960 A=0.87381 C=0.12619
gnomAD - Genomes American Sub 13634 A=0.72635 C=0.27365
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.6847 C=0.3153
gnomAD - Genomes East Asian Sub 3122 A=0.7505 C=0.2495
gnomAD - Genomes Other Sub 2152 A=0.7556 C=0.2444
8.3KJPN JAPANESE Study-wide 16758 A=0.78285 C=0.21715
1000Genomes Global Study-wide 5008 A=0.7935 C=0.2065
1000Genomes African Sub 1322 A=0.9077 C=0.0923
1000Genomes East Asian Sub 1008 A=0.7728 C=0.2272
1000Genomes Europe Sub 1006 A=0.7306 C=0.2694
1000Genomes South Asian Sub 978 A=0.777 C=0.223
1000Genomes American Sub 694 A=0.720 C=0.280
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.6589 C=0.3411
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7146 C=0.2854
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7222 C=0.2778
KOREAN population from KRGDB KOREAN Study-wide 2924 A=0.7671 C=0.2329
HapMap Global Study-wide 1890 A=0.8259 C=0.1741
HapMap American Sub 770 A=0.796 C=0.204
HapMap African Sub 690 A=0.884 C=0.116
HapMap Asian Sub 254 A=0.795 C=0.205
HapMap Europe Sub 176 A=0.773 C=0.227
Korean Genome Project KOREAN Study-wide 1832 A=0.7282 C=0.2718
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.701 C=0.299
Northern Sweden ACPOP Study-wide 600 A=0.630 C=0.370
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.811 C=0.189
SGDP_PRJ Global Study-wide 236 A=0.428 C=0.572
Qatari Global Study-wide 216 A=0.773 C=0.227
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.762 C=0.238
The Danish reference pan genome Danish Study-wide 40 A=0.72 C=0.28
Siberian Global Study-wide 28 A=0.39 C=0.61
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 A= C
GRCh38.p13 chr 1 NC_000001.11:g.156292862= NC_000001.11:g.156292862A>C
GRCh37.p13 chr 1 NC_000001.10:g.156262653= NC_000001.10:g.156262653A>C
GLMP transcript variant 1 NM_144580.3:c.*182= NM_144580.3:c.*182T>G
GLMP transcript variant 1 NM_144580.2:c.*182= NM_144580.2:c.*182T>G
GLMP transcript variant X1 XR_426762.3:n.1283= XR_426762.3:n.1283T>G
GLMP transcript variant X2 XM_011509117.3:c.*182= XM_011509117.3:c.*182T>G
GLMP transcript variant 5 NM_001256609.2:c.*182= NM_001256609.2:c.*182T>G
GLMP transcript variant 5 NM_001256609.1:c.*182= NM_001256609.1:c.*182T>G
GLMP transcript variant 2 NM_001256604.2:c.*182= NM_001256604.2:c.*182T>G
GLMP transcript variant 2 NM_001256604.1:c.*182= NM_001256604.1:c.*182T>G
GLMP transcript variant 4 NM_001256608.2:c.*150= NM_001256608.2:c.*150T>G
GLMP transcript variant 4 NM_001256608.1:c.*150= NM_001256608.1:c.*150T>G
GLMP transcript variant 3 NM_001256605.2:c.*182= NM_001256605.2:c.*182T>G
GLMP transcript variant 3 NM_001256605.1:c.*182= NM_001256605.1:c.*182T>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#.

62 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss8527 Sep 19, 2000 (52)
2 LEE ss1519757 Oct 13, 2000 (94)
3 YUSUKE ss4982106 Aug 28, 2002 (108)
4 CGAP-GAI ss16231642 Feb 27, 2004 (120)
5 ILLUMINA ss75063735 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss80750514 Dec 14, 2007 (130)
7 1000GENOMES ss108605416 Jan 23, 2009 (130)
8 1000GENOMES ss111167719 Jan 25, 2009 (130)
9 KRIBB_YJKIM ss119337928 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss164139361 Jul 04, 2010 (132)
11 ILLUMINA ss174119811 Jul 04, 2010 (132)
12 BUSHMAN ss199097355 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss205414068 Jul 04, 2010 (132)
14 1000GENOMES ss218655123 Jul 14, 2010 (132)
15 1000GENOMES ss230734790 Jul 14, 2010 (132)
16 1000GENOMES ss238381810 Jul 15, 2010 (132)
17 BL ss253515524 May 09, 2011 (134)
18 GMI ss276054123 May 04, 2012 (137)
19 ILLUMINA ss482109509 May 04, 2012 (137)
20 ILLUMINA ss484034733 May 04, 2012 (137)
21 TISHKOFF ss554713857 Apr 25, 2013 (138)
22 SSMP ss648419834 Apr 25, 2013 (138)
23 ILLUMINA ss782461940 Sep 08, 2015 (146)
24 EVA-GONL ss975692539 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1068275443 Aug 21, 2014 (142)
26 1000GENOMES ss1292968026 Aug 21, 2014 (142)
27 DDI ss1425980931 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1574396824 Apr 01, 2015 (144)
29 EVA_DECODE ss1585074343 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1601235220 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1644229253 Apr 01, 2015 (144)
32 EVA_MGP ss1710926649 Apr 01, 2015 (144)
33 EVA_SVP ss1712371643 Apr 01, 2015 (144)
34 WEILL_CORNELL_DGM ss1918926045 Feb 12, 2016 (147)
35 GENOMED ss1966869040 Jul 19, 2016 (147)
36 JJLAB ss2019978049 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148003725 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2166630672 Dec 20, 2016 (150)
39 TOPMED ss2329140634 Dec 20, 2016 (150)
40 GRF ss2697976340 Nov 08, 2017 (151)
41 GNOMAD ss2761449576 Nov 08, 2017 (151)
42 SWEGEN ss2987770090 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023745928 Nov 08, 2017 (151)
44 TOPMED ss3092454167 Nov 08, 2017 (151)
45 CSHL ss3343714443 Nov 08, 2017 (151)
46 ILLUMINA ss3637788251 Oct 11, 2018 (152)
47 ILLUMINA ss3642797470 Oct 11, 2018 (152)
48 EGCUT_WGS ss3655709143 Jul 12, 2019 (153)
49 EVA_DECODE ss3687803744 Jul 12, 2019 (153)
50 ACPOP ss3727493540 Jul 12, 2019 (153)
51 EVA ss3746820076 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3799820015 Jul 12, 2019 (153)
53 EVA ss3825576669 Apr 25, 2020 (154)
54 EVA ss3826428523 Apr 25, 2020 (154)
55 EVA ss3836608814 Apr 25, 2020 (154)
56 EVA ss3842018092 Apr 25, 2020 (154)
57 SGDP_PRJ ss3850026807 Apr 25, 2020 (154)
58 KRGDB ss3895241986 Apr 25, 2020 (154)
59 KOGIC ss3945676296 Apr 25, 2020 (154)
60 EVA ss4016938780 Apr 25, 2021 (155)
61 TOPMED ss4468709913 Apr 25, 2021 (155)
62 TOMMO_GENOMICS ss5146539305 Apr 25, 2021 (155)
63 1000Genomes NC_000001.10 - 156262653 Oct 11, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 156262653 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 156262653 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 156262653 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 156292862 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 156262653 Apr 25, 2020 (154)
69 HapMap NC_000001.11 - 156292862 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000001.10 - 156262653 Apr 25, 2020 (154)
71 Korean Genome Project NC_000001.11 - 156292862 Apr 25, 2020 (154)
72 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 156262653 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 156262653 Jul 12, 2019 (153)
74 Qatari NC_000001.10 - 156262653 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000001.10 - 156262653 Apr 25, 2020 (154)
76 Siberian NC_000001.10 - 156262653 Apr 25, 2020 (154)
77 8.3KJPN NC_000001.10 - 156262653 Apr 25, 2021 (155)
78 TopMed NC_000001.11 - 156292862 Apr 25, 2021 (155)
79 UK 10K study - Twins NC_000001.10 - 156262653 Oct 11, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000001.10 - 156262653 Jul 12, 2019 (153)
81 ALFA NC_000001.11 - 156292862 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)
rs1129578 Apr 12, 2001 (94)
rs3795729 Oct 08, 2002 (108)
rs56709873 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108605416, ss111167719, ss164139361, ss199097355, ss205414068, ss253515524, ss276054123, ss482109509, ss1585074343, ss1712371643, ss3642797470 NC_000001.9:154529276:A:C NC_000001.11:156292861:A:C (self)
3761549, 2044823, 1447391, 1711621, 887436, 2419380, 43401, 778405, 967975, 2043787, 520079, 4508612, 2044823, 438113, ss218655123, ss230734790, ss238381810, ss484034733, ss554713857, ss648419834, ss782461940, ss975692539, ss1068275443, ss1292968026, ss1425980931, ss1574396824, ss1601235220, ss1644229253, ss1710926649, ss1918926045, ss1966869040, ss2019978049, ss2148003725, ss2329140634, ss2697976340, ss2761449576, ss2987770090, ss3343714443, ss3637788251, ss3655709143, ss3727493540, ss3746820076, ss3825576669, ss3826428523, ss3836608814, ss3850026807, ss3895241986, ss4016938780, ss5146539305 NC_000001.10:156262652:A:C NC_000001.11:156292861:A:C (self)
27395706, 178071, 2054297, 20286972, 32316248, 4981427877, ss2166630672, ss3023745928, ss3092454167, ss3687803744, ss3799820015, ss3842018092, ss3945676296, ss4468709913 NC_000001.11:156292861:A:C NC_000001.11:156292861:A:C (self)
ss8527, ss1519757, ss4982106, ss16231642, ss75063735, ss80750514, ss119337928, ss174119811 NT_004487.19:7751294:A:C NC_000001.11:156292861:A: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 rs6800

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