Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1041938

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:134453973 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.246579 (65267/264690, TOPMED)
T=0.222402 (31155/140084, GnomAD)
T=0.15124 (2857/18890, ALFA) (+ 15 more)
T=0.38502 (6453/16760, 8.3KJPN)
T=0.3241 (1623/5008, 1000G)
T=0.0607 (272/4480, Estonian)
T=0.0589 (227/3854, ALSPAC)
T=0.0512 (190/3708, TWINSUK)
T=0.4392 (1287/2930, KOREAN)
T=0.4547 (833/1832, Korea1K)
T=0.053 (53/998, GoNL)
T=0.045 (27/600, NorthernSweden)
T=0.326 (107/328, HapMap)
A=0.358 (111/310, SGDP_PRJ)
T=0.440 (95/216, Qatari)
A=0.440 (95/216, Vietnamese)
T=0.05 (2/40, GENOME_DK)
A=0.40 (8/20, 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.134453973A>T
GRCh37.p13 chr 2 NC_000002.11:g.135211544A>T
MGAT5 RefSeqGene NG_030324.1:g.204715A>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.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant 1 NM_001371457.1:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X4 XM_011511200.1:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X1 XM_011511199.2:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X3 XM_006712534.3:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X5 XM_011511201.2:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X6 XM_005263670.3:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X10 XM_017004148.1:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X2 XM_017004147.2:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X8 XM_005263669.5:c.*5126= N/A 3 Prime UTR Variant
MGAT5 transcript variant X9 XM_011511202.2:c.*5126= 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 18890 A=0.84876 T=0.15124
European Sub 14286 A=0.93469 T=0.06531
African Sub 2946 A=0.4725 T=0.5275
African Others Sub 114 A=0.351 T=0.649
African American Sub 2832 A=0.4774 T=0.5226
Asian Sub 112 A=0.554 T=0.446
East Asian Sub 86 A=0.50 T=0.50
Other Asian Sub 26 A=0.73 T=0.27
Latin American 1 Sub 146 A=0.719 T=0.281
Latin American 2 Sub 610 A=0.838 T=0.162
South Asian Sub 98 A=0.83 T=0.17
Other Sub 692 A=0.764 T=0.236


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=0.753421 T=0.246579
gnomAD - Genomes Global Study-wide 140084 A=0.777598 T=0.222402
gnomAD - Genomes European Sub 75916 A=0.93640 T=0.06360
gnomAD - Genomes African Sub 41916 A=0.48743 T=0.51257
gnomAD - Genomes American Sub 13656 A=0.84344 T=0.15656
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.7920 T=0.2080
gnomAD - Genomes East Asian Sub 3124 A=0.5115 T=0.4885
gnomAD - Genomes Other Sub 2150 A=0.7735 T=0.2265
8.3KJPN JAPANESE Study-wide 16760 A=0.61498 T=0.38502
1000Genomes Global Study-wide 5008 A=0.6759 T=0.3241
1000Genomes African Sub 1322 A=0.4138 T=0.5862
1000Genomes East Asian Sub 1008 A=0.5149 T=0.4851
1000Genomes Europe Sub 1006 A=0.9145 T=0.0855
1000Genomes South Asian Sub 978 A=0.829 T=0.171
1000Genomes American Sub 694 A=0.847 T=0.153
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9393 T=0.0607
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9411 T=0.0589
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9488 T=0.0512
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5608 T=0.4392
Korean Genome Project KOREAN Study-wide 1832 A=0.5453 T=0.4547
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.947 T=0.053
Northern Sweden ACPOP Study-wide 600 A=0.955 T=0.045
HapMap Global Study-wide 328 A=0.674 T=0.326
HapMap African Sub 120 A=0.408 T=0.592
HapMap American Sub 120 A=0.967 T=0.033
HapMap Asian Sub 88 A=0.64 T=0.36
SGDP_PRJ Global Study-wide 310 A=0.358 T=0.642
Qatari Global Study-wide 216 A=0.560 T=0.440
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.440 T=0.560
The Danish reference pan genome Danish Study-wide 40 A=0.95 T=0.05
Siberian Global Study-wide 20 A=0.40 T=0.60
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= T
GRCh38.p13 chr 2 NC_000002.12:g.134453973= NC_000002.12:g.134453973A>T
GRCh37.p13 chr 2 NC_000002.11:g.135211544= NC_000002.11:g.135211544A>T
MGAT5 RefSeqGene NG_030324.1:g.204715= NG_030324.1:g.204715A>T
MGAT5 transcript variant 2 NM_002410.5:c.*5126= NM_002410.5:c.*5126A>T
MGAT5 transcript NM_002410.4:c.*5126= NM_002410.4:c.*5126A>T
MGAT5 transcript variant 1 NM_001371457.1:c.*5126= NM_001371457.1:c.*5126A>T
MGAT5 transcript variant X8 XM_005263669.5:c.*5126= XM_005263669.5:c.*5126A>T
MGAT5 transcript variant X6 XM_005263669.1:c.*5126= XM_005263669.1:c.*5126A>T
MGAT5 transcript variant X3 XM_006712534.3:c.*5126= XM_006712534.3:c.*5126A>T
MGAT5 transcript variant X6 XM_005263670.3:c.*5126= XM_005263670.3:c.*5126A>T
MGAT5 transcript variant X7 XM_005263670.1:c.*5126= XM_005263670.1:c.*5126A>T
MGAT5 transcript variant X1 XM_011511199.2:c.*5126= XM_011511199.2:c.*5126A>T
MGAT5 transcript variant X2 XM_017004147.2:c.*5126= XM_017004147.2:c.*5126A>T
MGAT5 transcript variant X5 XM_011511201.2:c.*5126= XM_011511201.2:c.*5126A>T
MGAT5 transcript variant X9 XM_011511202.2:c.*5126= XM_011511202.2:c.*5126A>T
MGAT5 transcript variant X10 XM_017004148.1:c.*5126= XM_017004148.1:c.*5126A>T
MGAT5 transcript variant X4 XM_011511200.1:c.*5126= XM_011511200.1:c.*5126A>T
LOC151162 transcript NR_024275.1:n.4585= NR_024275.1:n.4585A>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#.

59 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1508759 Oct 05, 2000 (86)
2 WI_SSAHASNP ss11440276 Jul 11, 2003 (116)
3 CGAP-GAI ss16244305 Feb 27, 2004 (120)
4 SEQUENOM ss24812461 Sep 20, 2004 (123)
5 HGSV ss86142065 Dec 16, 2007 (130)
6 BGI ss103590562 Dec 01, 2009 (131)
7 ILLUMINA-UK ss117885345 Feb 14, 2009 (130)
8 BUSHMAN ss201088175 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss205882205 Jul 04, 2010 (132)
10 1000GENOMES ss211003539 Jul 14, 2010 (132)
11 1000GENOMES ss219524261 Jul 14, 2010 (132)
12 1000GENOMES ss231371587 Jul 14, 2010 (132)
13 1000GENOMES ss238877986 Jul 15, 2010 (132)
14 GMI ss276690523 May 04, 2012 (137)
15 PJP ss292372922 May 09, 2011 (134)
16 TISHKOFF ss555891862 Apr 25, 2013 (138)
17 SSMP ss649519127 Apr 25, 2013 (138)
18 EVA-GONL ss977383371 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1069514224 Aug 21, 2014 (142)
20 1000GENOMES ss1299424934 Aug 21, 2014 (142)
21 DDI ss1428748186 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1579096675 Apr 01, 2015 (144)
23 EVA_DECODE ss1586811660 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1604615581 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1647609614 Apr 01, 2015 (144)
26 HAMMER_LAB ss1797569073 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1920641611 Feb 12, 2016 (147)
28 GENOMED ss1968894482 Jul 19, 2016 (147)
29 JJLAB ss2020844879 Sep 14, 2016 (149)
30 USC_VALOUEV ss2148910522 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2234473445 Dec 20, 2016 (150)
32 TOPMED ss2400832463 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624928958 Nov 08, 2017 (151)
34 GRF ss2703534710 Nov 08, 2017 (151)
35 GNOMAD ss2779937311 Nov 08, 2017 (151)
36 AFFY ss2985806967 Nov 08, 2017 (151)
37 SWEGEN ss2990468793 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3024185804 Nov 08, 2017 (151)
39 TOPMED ss3323615271 Nov 08, 2017 (151)
40 CSHL ss3344492964 Nov 08, 2017 (151)
41 OMUKHERJEE_ADBS ss3646272780 Oct 11, 2018 (152)
42 EGCUT_WGS ss3658310216 Jul 13, 2019 (153)
43 EVA_DECODE ss3704939641 Jul 13, 2019 (153)
44 ACPOP ss3728888650 Jul 13, 2019 (153)
45 EVA ss3757411191 Jul 13, 2019 (153)
46 PACBIO ss3784000902 Jul 13, 2019 (153)
47 PACBIO ss3789563592 Jul 13, 2019 (153)
48 PACBIO ss3794436535 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3801779066 Jul 13, 2019 (153)
50 EVA ss3825609371 Apr 25, 2020 (154)
51 EVA ss3827233247 Apr 25, 2020 (154)
52 SGDP_PRJ ss3853465853 Apr 25, 2020 (154)
53 KRGDB ss3899024811 Apr 25, 2020 (154)
54 KOGIC ss3949016236 Apr 25, 2020 (154)
55 FSA-LAB ss3984189358 Apr 26, 2021 (155)
56 FSA-LAB ss3984189359 Apr 26, 2021 (155)
57 EVA ss3986019629 Apr 26, 2021 (155)
58 TOPMED ss4524766776 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5153975573 Apr 26, 2021 (155)
60 1000Genomes NC_000002.11 - 135211544 Oct 11, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 135211544 Oct 11, 2018 (152)
62 Genetic variation in the Estonian population NC_000002.11 - 135211544 Oct 11, 2018 (152)
63 The Danish reference pan genome NC_000002.11 - 135211544 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000002.12 - 134453973 Apr 26, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000002.11 - 135211544 Apr 25, 2020 (154)
66 HapMap NC_000002.12 - 134453973 Apr 25, 2020 (154)
67 KOREAN population from KRGDB NC_000002.11 - 135211544 Apr 25, 2020 (154)
68 Korean Genome Project NC_000002.12 - 134453973 Apr 25, 2020 (154)
69 Northern Sweden NC_000002.11 - 135211544 Jul 13, 2019 (153)
70 Qatari NC_000002.11 - 135211544 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000002.11 - 135211544 Apr 25, 2020 (154)
72 Siberian NC_000002.11 - 135211544 Apr 25, 2020 (154)
73 8.3KJPN NC_000002.11 - 135211544 Apr 26, 2021 (155)
74 TopMed NC_000002.12 - 134453973 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000002.11 - 135211544 Oct 11, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000002.11 - 135211544 Jul 13, 2019 (153)
77 ALFA NC_000002.12 - 134453973 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)
rs61440406 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss86142065 NC_000002.9:135045275:A:T NC_000002.12:134453972:A:T (self)
ss117885345, ss201088175, ss205882205, ss211003539, ss276690523, ss292372922, ss1586811660 NC_000002.10:134928013:A:T NC_000002.12:134453972:A:T (self)
10444218, 5752728, 4048464, 5261614, 2529447, 6202205, 2173515, 2683541, 5482833, 1426876, 11944880, 5752728, 1244805, ss219524261, ss231371587, ss238877986, ss555891862, ss649519127, ss977383371, ss1069514224, ss1299424934, ss1428748186, ss1579096675, ss1604615581, ss1647609614, ss1797569073, ss1920641611, ss1968894482, ss2020844879, ss2148910522, ss2400832463, ss2624928958, ss2703534710, ss2779937311, ss2985806967, ss2990468793, ss3344492964, ss3646272780, ss3658310216, ss3728888650, ss3757411191, ss3784000902, ss3789563592, ss3794436535, ss3825609371, ss3827233247, ss3853465853, ss3899024811, ss3984189358, ss3984189359, ss3986019629, ss5153975573 NC_000002.11:135211543:A:T NC_000002.12:134453972:A:T (self)
74460294, 1898435, 5394237, 205008773, 328589655, 8533497308, ss2234473445, ss3024185804, ss3323615271, ss3704939641, ss3801779066, ss3949016236, ss4524766776 NC_000002.12:134453972:A:T NC_000002.12:134453972:A:T (self)
ss11440276 NT_005058.13:3820442:A:T NC_000002.12:134453972:A:T (self)
ss1508759, ss16244305, ss24812461, ss103590562 NT_022135.16:24960206:A:T NC_000002.12:134453972:A: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 rs1041938

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