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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.

rs4147606

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:165654214 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.262670 (69526/264690, TOPMED)
T=0.231173 (32367/140012, GnomAD)
T=0.19047 (5863/30782, ALFA) (+ 15 more)
C=0.15507 (2599/16760, 8.3KJPN)
T=0.4217 (2112/5008, 1000G)
T=0.1763 (790/4480, Estonian)
T=0.1440 (555/3854, ALSPAC)
T=0.1405 (521/3708, TWINSUK)
C=0.1631 (478/2930, KOREAN)
T=0.4105 (775/1888, HapMap)
T=0.143 (143/998, GoNL)
T=0.202 (121/600, NorthernSweden)
T=0.129 (69/534, MGP)
C=0.284 (105/370, SGDP_PRJ)
T=0.264 (57/216, Qatari)
C=0.215 (46/214, Vietnamese)
T=0.15 (6/40, GENOME_DK)
C=0.35 (14/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MGST3 : 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.p13 chr 1 NC_000001.11:g.165654214C>G
GRCh38.p13 chr 1 NC_000001.11:g.165654214C>T
GRCh37.p13 chr 1 NC_000001.10:g.165623451C>G
GRCh37.p13 chr 1 NC_000001.10:g.165623451C>T
Gene: MGST3, microsomal glutathione S-transferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MGST3 transcript NM_004528.4:c.250-65C>G N/A Intron Variant
MGST3 transcript variant X1 XM_005245174.3:c.250-65C>G 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

ALFA Allele Frequency (New)
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 30782 C=0.80953 T=0.19047
European Sub 23982 C=0.85001 T=0.14999
African Sub 4246 C=0.6969 T=0.3031
African Others Sub 168 C=0.720 T=0.280
African American Sub 4078 C=0.6959 T=0.3041
Asian Sub 128 C=0.273 T=0.727
East Asian Sub 98 C=0.23 T=0.77
Other Asian Sub 30 C=0.40 T=0.60
Latin American 1 Sub 242 C=0.744 T=0.256
Latin American 2 Sub 1210 C=0.5529 T=0.4471
South Asian Sub 120 C=0.617 T=0.383
Other Sub 854 C=0.722 T=0.278


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=0.737330 T=0.262670
gnomAD - Genomes Global Study-wide 140012 C=0.768827 T=0.231173
gnomAD - Genomes European Sub 75834 C=0.85401 T=0.14599
gnomAD - Genomes African Sub 41944 C=0.68205 T=0.31795
gnomAD - Genomes American Sub 13636 C=0.66882 T=0.33118
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8913 T=0.1087
gnomAD - Genomes East Asian Sub 3126 C=0.1859 T=0.8141
gnomAD - Genomes Other Sub 2150 C=0.7498 T=0.2502
8.3KJPN JAPANESE Study-wide 16760 C=0.15507 T=0.84493
1000Genomes Global Study-wide 5008 C=0.5783 T=0.4217
1000Genomes African Sub 1322 C=0.6725 T=0.3275
1000Genomes East Asian Sub 1008 C=0.1825 T=0.8175
1000Genomes Europe Sub 1006 C=0.8718 T=0.1282
1000Genomes South Asian Sub 978 C=0.563 T=0.437
1000Genomes American Sub 694 C=0.569 T=0.431
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8237 T=0.1763
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8560 T=0.1440
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8595 T=0.1405
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.1631 G=0.0000, T=0.8369
HapMap Global Study-wide 1888 C=0.5895 T=0.4105
HapMap American Sub 770 C=0.592 T=0.408
HapMap African Sub 692 C=0.671 T=0.329
HapMap Asian Sub 252 C=0.155 T=0.845
HapMap Europe Sub 174 C=0.885 T=0.115
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.857 T=0.143
Northern Sweden ACPOP Study-wide 600 C=0.798 T=0.202
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.871 T=0.129
SGDP_PRJ Global Study-wide 370 C=0.284 T=0.716
Qatari Global Study-wide 216 C=0.736 T=0.264
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.215 T=0.785
The Danish reference pan genome Danish Study-wide 40 C=0.85 T=0.15
Siberian Global Study-wide 40 C=0.35 T=0.65
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= G T
GRCh38.p13 chr 1 NC_000001.11:g.165654214= NC_000001.11:g.165654214C>G NC_000001.11:g.165654214C>T
GRCh37.p13 chr 1 NC_000001.10:g.165623451= NC_000001.10:g.165623451C>G NC_000001.10:g.165623451C>T
MGST3 transcript NM_004528.3:c.250-65= NM_004528.3:c.250-65C>G NM_004528.3:c.250-65C>T
MGST3 transcript NM_004528.4:c.250-65= NM_004528.4:c.250-65C>G NM_004528.4:c.250-65C>T
MGST3 transcript variant X1 XM_005245174.1:c.292-65= XM_005245174.1:c.292-65C>G XM_005245174.1:c.292-65C>T
MGST3 transcript variant X1 XM_005245174.3:c.250-65= XM_005245174.3:c.250-65C>G XM_005245174.3:c.250-65C>T
MGST3 transcript variant X2 XM_005245175.1:c.250-72= XM_005245175.1:c.250-72C>G XM_005245175.1:c.250-72C>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#.

72 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 RIKENSNPRC ss5600988 Dec 16, 2002 (110)
2 EGP_SNPS ss12709431 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss19846545 Feb 27, 2004 (120)
4 SSAHASNP ss20527537 Apr 05, 2004 (121)
5 PERLEGEN ss23160617 Sep 20, 2004 (123)
6 ILLUMINA ss65760314 Oct 15, 2006 (127)
7 ILLUMINA ss74889341 Dec 06, 2007 (129)
8 HUMANGENOME_JCVI ss97980988 Feb 06, 2009 (130)
9 BGI ss106607489 Feb 06, 2009 (130)
10 ILLUMINA-UK ss119068564 Feb 15, 2009 (130)
11 KRIBB_YJKIM ss119471059 Dec 01, 2009 (131)
12 ENSEMBL ss139184672 Dec 01, 2009 (131)
13 ILLUMINA ss152536444 Dec 01, 2009 (131)
14 GMI ss155864681 Dec 01, 2009 (131)
15 ILLUMINA ss159102640 Dec 01, 2009 (131)
16 ILLUMINA ss168871011 Jul 04, 2010 (132)
17 ILLUMINA ss173692495 Jul 04, 2010 (132)
18 BUSHMAN ss199182892 Jul 04, 2010 (132)
19 1000GENOMES ss210658959 Jul 14, 2010 (132)
20 1000GENOMES ss218692124 Jul 14, 2010 (132)
21 1000GENOMES ss230762563 Jul 14, 2010 (132)
22 1000GENOMES ss238404671 Jul 15, 2010 (132)
23 BL ss253569645 May 09, 2011 (134)
24 GMI ss276083593 May 04, 2012 (137)
25 PJP ss290653577 May 09, 2011 (134)
26 TISHKOFF ss554796538 Apr 25, 2013 (138)
27 SSMP ss648467755 Apr 25, 2013 (138)
28 ILLUMINA ss832615436 Jul 12, 2019 (153)
29 EVA-GONL ss975764679 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1068328545 Aug 21, 2014 (142)
31 1000GENOMES ss1293237446 Aug 21, 2014 (142)
32 EVA_GENOME_DK ss1574445420 Apr 01, 2015 (144)
33 EVA_DECODE ss1585149142 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1601379667 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1644373700 Apr 01, 2015 (144)
36 EVA_MGP ss1710930890 Apr 01, 2015 (144)
37 EVA_SVP ss1712377642 Apr 01, 2015 (144)
38 HAMMER_LAB ss1795201381 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1919000926 Feb 12, 2016 (147)
40 GENOMED ss1966886694 Jul 19, 2016 (147)
41 JJLAB ss2020015742 Sep 14, 2016 (149)
42 USC_VALOUEV ss2148042686 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2167163110 Dec 20, 2016 (150)
44 TOPMED ss2329696790 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2624516948 Nov 08, 2017 (151)
46 GRF ss2698019812 Nov 08, 2017 (151)
47 GNOMAD ss2762197316 Nov 08, 2017 (151)
48 SWEGEN ss2987879345 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3023765518 Nov 08, 2017 (151)
50 TOPMED ss3094160846 Nov 08, 2017 (151)
51 CSHL ss3343747383 Nov 08, 2017 (151)
52 ILLUMINA ss3637792777 Oct 11, 2018 (152)
53 ILLUMINA ss3637792778 Oct 11, 2018 (152)
54 ILLUMINA ss3642801507 Oct 11, 2018 (152)
55 OMUKHERJEE_ADBS ss3646248169 Oct 11, 2018 (152)
56 URBANLAB ss3646808952 Oct 11, 2018 (152)
57 EGCUT_WGS ss3655821041 Jul 12, 2019 (153)
58 EVA_DECODE ss3687935465 Jul 12, 2019 (153)
59 ACPOP ss3727554347 Jul 12, 2019 (153)
60 EVA ss3746904165 Jul 12, 2019 (153)
61 KHV_HUMAN_GENOMES ss3799904254 Jul 12, 2019 (153)
62 EVA ss3825579516 Apr 25, 2020 (154)
63 EVA ss3826465607 Apr 25, 2020 (154)
64 EVA ss3836628305 Apr 25, 2020 (154)
65 EVA ss3842038066 Apr 25, 2020 (154)
66 SGDP_PRJ ss3850166924 Apr 25, 2020 (154)
67 KRGDB ss3895397609 Apr 25, 2020 (154)
68 FSA-LAB ss3983952231 Apr 25, 2021 (155)
69 FSA-LAB ss3983952232 Apr 25, 2021 (155)
70 EVA ss3986145376 Apr 25, 2021 (155)
71 TOPMED ss4471024923 Apr 25, 2021 (155)
72 TOMMO_GENOMICS ss5146838630 Apr 25, 2021 (155)
73 1000Genomes NC_000001.10 - 165623451 Oct 11, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 165623451 Oct 11, 2018 (152)
75 Genetic variation in the Estonian population NC_000001.10 - 165623451 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000001.10 - 165623451 Apr 25, 2020 (154)
77 gnomAD - Genomes NC_000001.11 - 165654214 Apr 25, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000001.10 - 165623451 Apr 25, 2020 (154)
79 HapMap NC_000001.11 - 165654214 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 165623451 Apr 25, 2020 (154)
81 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 165623451 Apr 25, 2020 (154)
82 Northern Sweden NC_000001.10 - 165623451 Jul 12, 2019 (153)
83 Qatari NC_000001.10 - 165623451 Apr 25, 2020 (154)
84 SGDP_PRJ NC_000001.10 - 165623451 Apr 25, 2020 (154)
85 Siberian NC_000001.10 - 165623451 Apr 25, 2020 (154)
86 8.3KJPN NC_000001.10 - 165623451 Apr 25, 2021 (155)
87 TopMed NC_000001.11 - 165654214 Apr 25, 2021 (155)
88 UK 10K study - Twins NC_000001.10 - 165623451 Oct 11, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000001.10 - 165623451 Jul 12, 2019 (153)
90 ALFA NC_000001.11 - 165654214 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
2575003, ss3895397609 NC_000001.10:165623450:C:G NC_000001.11:165654213:C:G (self)
ss119068564, ss199182892, ss210658959, ss253569645, ss276083593, ss290653577, ss1585149142, ss1712377642, ss3642801507 NC_000001.9:163890074:C:T NC_000001.11:165654213:C:T (self)
4039868, 2202683, 1559289, 1740598, 957700, 2575003, 47642, 839212, 1042856, 2183904, 559040, 4807937, 2202683, 473410, ss218692124, ss230762563, ss238404671, ss554796538, ss648467755, ss832615436, ss975764679, ss1068328545, ss1293237446, ss1574445420, ss1601379667, ss1644373700, ss1710930890, ss1795201381, ss1919000926, ss1966886694, ss2020015742, ss2148042686, ss2329696790, ss2624516948, ss2698019812, ss2762197316, ss2987879345, ss3343747383, ss3637792777, ss3637792778, ss3646248169, ss3655821041, ss3727554347, ss3746904165, ss3825579516, ss3826465607, ss3836628305, ss3850166924, ss3895397609, ss3983952231, ss3983952232, ss3986145376, ss5146838630 NC_000001.10:165623450:C:T NC_000001.11:165654213:C:T (self)
29291551, 193733, 21736692, 34631258, 9978065966, ss2167163110, ss3023765518, ss3094160846, ss3646808952, ss3687935465, ss3799904254, ss3842038066, ss4471024923 NC_000001.11:165654213:C:T NC_000001.11:165654213:C:T (self)
ss5600988, ss12709431, ss23160617, ss65760314, ss74889341, ss97980988, ss106607489, ss119471059, ss139184672, ss152536444, ss155864681, ss159102640, ss168871011, ss173692495 NT_004487.19:17112092:C:T NC_000001.11:165654213:C:T (self)
ss19846545, ss20527537 NT_004668.16:4128922:C:T NC_000001.11:165654213: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 rs4147606

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