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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.

rs7841

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:134454290 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.068155 (18040/264690, TOPMED)
T=0.067845 (9509/140158, GnomAD)
T=0.08491 (2620/30858, ALFA) (+ 14 more)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0449 (225/5008, 1000G)
T=0.0542 (243/4480, Estonian)
T=0.0908 (350/3854, ALSPAC)
T=0.1017 (377/3708, TWINSUK)
T=0.098 (98/998, GoNL)
T=0.088 (53/600, NorthernSweden)
T=0.037 (8/216, Qatari)
T=0.11 (8/72, Ancient Sardinia)
T=0.12 (5/40, GENOME_DK)
C=0.50 (15/30, SGDP_PRJ)
T=0.50 (15/30, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MGAT5 : 3 Prime UTR 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 2 NC_000002.12:g.134454290C>T
GRCh37.p13 chr 2 NC_000002.11:g.135211861C>T
MGAT5 RefSeqGene NG_030324.1:g.205032C>T
Gene: MGAT5, alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MGAT5 transcript variant 2 NM_002410.5:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant 1 NM_001371457.1:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X4 XM_011511200.1:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X1 XM_011511199.2:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X3 XM_006712534.3:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X5 XM_011511201.2:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X6 XM_005263670.3:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X10 XM_017004148.1:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X2 XM_017004147.2:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X8 XM_005263669.5:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X9 XM_011511202.2:c.*5443= N/A 3 Prime UTR Variant
MGAT5 transcript variant X11 XM_011511204.2:c. N/A Genic Downstream Transcript Variant
MGAT5 transcript variant X12 XM_017004149.1:c. N/A Genic 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 30858 C=0.91509 T=0.08491
European Sub 24728 C=0.90909 T=0.09091
African Sub 3168 C=0.9615 T=0.0385
African Others Sub 124 C=0.952 T=0.048
African American Sub 3044 C=0.9619 T=0.0381
Asian Sub 128 C=0.992 T=0.008
East Asian Sub 100 C=0.99 T=0.01
Other Asian Sub 28 C=1.00 T=0.00
Latin American 1 Sub 168 C=0.935 T=0.065
Latin American 2 Sub 700 C=0.927 T=0.073
South Asian Sub 114 C=0.974 T=0.026
Other Sub 1852 C=0.9006 T=0.0994


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 C=0.931845 T=0.068155
gnomAD - Genomes Global Study-wide 140158 C=0.932155 T=0.067845
gnomAD - Genomes European Sub 75918 C=0.91582 T=0.08418
gnomAD - Genomes African Sub 41980 C=0.96582 T=0.03418
gnomAD - Genomes American Sub 13652 C=0.92836 T=0.07164
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8377 T=0.1623
gnomAD - Genomes East Asian Sub 3132 C=0.9981 T=0.0019
gnomAD - Genomes Other Sub 2154 C=0.9257 T=0.0743
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
1000Genomes Global Study-wide 5008 C=0.9551 T=0.0449
1000Genomes African Sub 1322 C=0.9697 T=0.0303
1000Genomes East Asian Sub 1008 C=0.9990 T=0.0010
1000Genomes Europe Sub 1006 C=0.9085 T=0.0915
1000Genomes South Asian Sub 978 C=0.945 T=0.055
1000Genomes American Sub 694 C=0.945 T=0.055
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9458 T=0.0542
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9092 T=0.0908
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8983 T=0.1017
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.902 T=0.098
Northern Sweden ACPOP Study-wide 600 C=0.912 T=0.088
Qatari Global Study-wide 216 C=0.963 T=0.037
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 72 C=0.89 T=0.11
The Danish reference pan genome Danish Study-wide 40 C=0.88 T=0.12
SGDP_PRJ Global Study-wide 30 C=0.50 T=0.50
Siberian Global Study-wide 2 C=0.5 T=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 C= T
GRCh38.p13 chr 2 NC_000002.12:g.134454290= NC_000002.12:g.134454290C>T
GRCh37.p13 chr 2 NC_000002.11:g.135211861= NC_000002.11:g.135211861C>T
MGAT5 RefSeqGene NG_030324.1:g.205032= NG_030324.1:g.205032C>T
MGAT5 transcript variant 2 NM_002410.5:c.*5443= NM_002410.5:c.*5443C>T
MGAT5 transcript NM_002410.4:c.*5443= NM_002410.4:c.*5443C>T
MGAT5 transcript variant 1 NM_001371457.1:c.*5443= NM_001371457.1:c.*5443C>T
MGAT5 transcript variant X8 XM_005263669.5:c.*5443= XM_005263669.5:c.*5443C>T
MGAT5 transcript variant X6 XM_005263669.1:c.*5443= XM_005263669.1:c.*5443C>T
MGAT5 transcript variant X3 XM_006712534.3:c.*5443= XM_006712534.3:c.*5443C>T
MGAT5 transcript variant X6 XM_005263670.3:c.*5443= XM_005263670.3:c.*5443C>T
MGAT5 transcript variant X7 XM_005263670.1:c.*5443= XM_005263670.1:c.*5443C>T
MGAT5 transcript variant X1 XM_011511199.2:c.*5443= XM_011511199.2:c.*5443C>T
MGAT5 transcript variant X2 XM_017004147.2:c.*5443= XM_017004147.2:c.*5443C>T
MGAT5 transcript variant X5 XM_011511201.2:c.*5443= XM_011511201.2:c.*5443C>T
MGAT5 transcript variant X9 XM_011511202.2:c.*5443= XM_011511202.2:c.*5443C>T
MGAT5 transcript variant X10 XM_017004148.1:c.*5443= XM_017004148.1:c.*5443C>T
MGAT5 transcript variant X4 XM_011511200.1:c.*5443= XM_011511200.1:c.*5443C>T
LOC151162 transcript NR_024275.1:n.4902= NR_024275.1:n.4902C>T
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#.

50 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss9767 Sep 19, 2000 (52)
2 LEE ss1508768 Oct 04, 2000 (86)
3 LEE ss4390536 May 29, 2002 (106)
4 LEE ss4403195 May 29, 2002 (106)
5 CGAP-GAI ss16244304 Feb 27, 2004 (120)
6 1000GENOMES ss109909890 Jan 24, 2009 (130)
7 1000GENOMES ss219524263 Jul 14, 2010 (132)
8 1000GENOMES ss231371589 Jul 14, 2010 (132)
9 ILLUMINA ss483910744 May 04, 2012 (137)
10 ILLUMINA ss484142070 May 04, 2012 (137)
11 ILLUMINA ss536331865 Sep 08, 2015 (146)
12 ILLUMINA ss780542553 Sep 08, 2015 (146)
13 ILLUMINA ss782516675 Sep 08, 2015 (146)
14 ILLUMINA ss836034422 Sep 08, 2015 (146)
15 EVA-GONL ss977383375 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1069514229 Aug 21, 2014 (142)
17 1000GENOMES ss1299424944 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1579096677 Apr 01, 2015 (144)
19 EVA_DECODE ss1586811662 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1604615587 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1647609620 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1920641615 Feb 12, 2016 (147)
23 JJLAB ss2020844881 Sep 14, 2016 (149)
24 USC_VALOUEV ss2148910524 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2234473470 Dec 20, 2016 (150)
26 TOPMED ss2400832491 Dec 20, 2016 (150)
27 ILLUMINA ss2633675934 Nov 08, 2017 (151)
28 GNOMAD ss2779937341 Nov 08, 2017 (151)
29 AFFY ss2985806970 Nov 08, 2017 (151)
30 SWEGEN ss2990468798 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3024185805 Nov 08, 2017 (151)
32 TOPMED ss3323615330 Nov 08, 2017 (151)
33 CSHL ss3344492966 Nov 08, 2017 (151)
34 ILLUMINA ss3628170896 Oct 11, 2018 (152)
35 ILLUMINA ss3631639414 Oct 11, 2018 (152)
36 ILLUMINA ss3642125829 Oct 11, 2018 (152)
37 OMUKHERJEE_ADBS ss3646272783 Oct 11, 2018 (152)
38 EGCUT_WGS ss3658310223 Jul 13, 2019 (153)
39 EVA_DECODE ss3704939646 Jul 13, 2019 (153)
40 ACPOP ss3728888652 Jul 13, 2019 (153)
41 EVA ss3757411198 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3801779071 Jul 13, 2019 (153)
43 EVA ss3825609372 Apr 25, 2020 (154)
44 EVA ss3827233250 Apr 25, 2020 (154)
45 EVA ss3837032124 Apr 25, 2020 (154)
46 EVA ss3842450728 Apr 25, 2020 (154)
47 SGDP_PRJ ss3853465861 Apr 25, 2020 (154)
48 EVA ss3984923229 Apr 26, 2021 (155)
49 TOPMED ss4524766868 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5153975589 Apr 26, 2021 (155)
51 1000Genomes NC_000002.11 - 135211861 Oct 11, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 135211861 Oct 11, 2018 (152)
53 Genetic variation in the Estonian population NC_000002.11 - 135211861 Oct 11, 2018 (152)
54 The Danish reference pan genome NC_000002.11 - 135211861 Apr 25, 2020 (154)
55 gnomAD - Genomes NC_000002.12 - 134454290 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000002.11 - 135211861 Apr 25, 2020 (154)
57 Northern Sweden NC_000002.11 - 135211861 Jul 13, 2019 (153)
58 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 135211861 Apr 26, 2021 (155)
59 Qatari NC_000002.11 - 135211861 Apr 25, 2020 (154)
60 SGDP_PRJ NC_000002.11 - 135211861 Apr 25, 2020 (154)
61 Siberian NC_000002.11 - 135211861 Apr 25, 2020 (154)
62 8.3KJPN NC_000002.11 - 135211861 Apr 26, 2021 (155)
63 TopMed NC_000002.12 - 134454290 Apr 26, 2021 (155)
64 UK 10K study - Twins NC_000002.11 - 135211861 Oct 11, 2018 (152)
65 ALFA NC_000002.12 - 134454290 Apr 26, 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)
rs3174945 Jul 03, 2002 (106)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109909890, ss483910744, ss1586811662 NC_000002.10:134928330:C:T NC_000002.12:134454289:C:T (self)
10444229, 5752734, 4048471, 5261616, 2529451, 2173517, 149156, 2683545, 5482841, 1426878, 11944896, 5752734, ss219524263, ss231371589, ss484142070, ss536331865, ss780542553, ss782516675, ss836034422, ss977383375, ss1069514229, ss1299424944, ss1579096677, ss1604615587, ss1647609620, ss1920641615, ss2020844881, ss2148910524, ss2400832491, ss2633675934, ss2779937341, ss2985806970, ss2990468798, ss3344492966, ss3628170896, ss3631639414, ss3642125829, ss3646272783, ss3658310223, ss3728888652, ss3757411198, ss3825609372, ss3827233250, ss3837032124, ss3853465861, ss3984923229, ss5153975589 NC_000002.11:135211860:C:T NC_000002.12:134454289:C:T (self)
74460361, 205008829, 328589747, 15132606229, ss2234473470, ss3024185805, ss3323615330, ss3704939646, ss3801779071, ss3842450728, ss4524766868 NC_000002.12:134454289:C:T NC_000002.12:134454289:C:T (self)
ss9767, ss1508768, ss4390536, ss4403195, ss16244304 NT_022135.16:24960523:C:T NC_000002.12:134454289:C: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 rs7841

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