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.

rs3817627

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120650728 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.340398 (85508/251200, GnomAD_exome)
T=0.408313 (51271/125568, TOPMED)
T=0.343511 (41672/121312, ExAC) (+ 18 more)
T=0.41161 (12899/31338, GnomAD)
T=0.37925 (5440/14344, ALFA Project)
T=0.42914 (5578/12998, GO-ESP)
T=0.3966 (1986/5008, 1000G)
T=0.3551 (1591/4480, Estonian)
T=0.3256 (1255/3854, ALSPAC)
T=0.3188 (1182/3708, TWINSUK)
T=0.1939 (568/2930, KOREAN)
T=0.4461 (844/1892, HapMap)
T=0.2025 (371/1832, Korea1K)
T=0.307 (306/998, GoNL)
T=0.353 (212/600, NorthernSweden)
T=0.371 (198/534, MGP)
T=0.227 (110/484, SGDP_PRJ)
G=0.481 (104/216, Qatari)
T=0.192 (41/214, Vietnamese)
T=0.17 (8/46, Siberian)
T=0.23 (9/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Intron Variant
Publications
1 citation
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 3 NC_000003.12:g.120650728T>G
GRCh37.p13 chr 3 NC_000003.11:g.120369575T>G
HGD RefSeqGene NG_011957.1:g.36754A>C
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.434+46A>C N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.434+46A>C N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c.434+46A>C N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c.434+46A>C N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c.434+46A>C N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.11+46A>C 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 41658 T=0.37366 G=0.62634
European Sub 32578 T=0.34928 G=0.65072
African Sub 3776 T=0.5829 G=0.4171
African Others Sub 132 T=0.545 G=0.455
African American Sub 3644 T=0.5842 G=0.4158
Asian Sub 184 T=0.179 G=0.821
East Asian Sub 126 T=0.183 G=0.817
Other Asian Sub 58 T=0.17 G=0.83
Latin American 1 Sub 168 T=0.482 G=0.518
Latin American 2 Sub 700 T=0.304 G=0.696
South Asian Sub 114 T=0.307 G=0.693
Other Sub 4138 T=0.3925 G=0.6075


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
gnomAD - Exomes Global Study-wide 251200 T=0.340398 G=0.659602
gnomAD - Exomes European Sub 135196 T=0.338072 G=0.661928
gnomAD - Exomes Asian Sub 48980 T=0.26174 G=0.73826
gnomAD - Exomes American Sub 34578 T=0.28689 G=0.71311
gnomAD - Exomes African Sub 16248 T=0.61614 G=0.38386
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=0.48570 G=0.51430
gnomAD - Exomes Other Sub 6130 T=0.3525 G=0.6475
TopMed Global Study-wide 125568 T=0.408313 G=0.591687
ExAC Global Study-wide 121312 T=0.343511 G=0.656489
ExAC Europe Sub 73306 T=0.34270 G=0.65730
ExAC Asian Sub 25130 T=0.26761 G=0.73239
ExAC American Sub 11570 T=0.27329 G=0.72671
ExAC African Sub 10398 T=0.61118 G=0.38882
ExAC Other Sub 908 T=0.339 G=0.661
gnomAD - Genomes Global Study-wide 31338 T=0.41161 G=0.58839
gnomAD - Genomes European Sub 18870 T=0.34542 G=0.65458
gnomAD - Genomes African Sub 8692 T=0.6079 G=0.3921
gnomAD - Genomes East Asian Sub 1554 T=0.1873 G=0.8127
gnomAD - Genomes Other Sub 1088 T=0.3768 G=0.6232
gnomAD - Genomes American Sub 846 T=0.293 G=0.707
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.514 G=0.486
ALFA Total Global 14344 T=0.37925 G=0.62075
ALFA European Sub 11082 T=0.36907 G=0.63093
ALFA Other Sub 2422 T=0.3869 G=0.6131
ALFA African Sub 754 T=0.533 G=0.467
ALFA Asian Sub 68 T=0.12 G=0.88
ALFA Latin American 2 Sub 12 T=0.25 G=0.75
ALFA South Asian Sub 4 T=0.0 G=1.0
ALFA Latin American 1 Sub 2 T=0.0 G=1.0
GO Exome Sequencing Project Global Study-wide 12998 T=0.42914 G=0.57086
GO Exome Sequencing Project European American Sub 8592 T=0.3408 G=0.6592
GO Exome Sequencing Project African American Sub 4406 T=0.6015 G=0.3985
1000Genomes Global Study-wide 5008 T=0.3966 G=0.6034
1000Genomes African Sub 1322 T=0.6861 G=0.3139
1000Genomes East Asian Sub 1008 T=0.2024 G=0.7976
1000Genomes Europe Sub 1006 T=0.3598 G=0.6402
1000Genomes South Asian Sub 978 T=0.279 G=0.721
1000Genomes American Sub 694 T=0.346 G=0.654
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.3551 G=0.6449
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3256 G=0.6744
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3188 G=0.6812
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.1939 G=0.8061
HapMap Global Study-wide 1892 T=0.4461 G=0.5539
HapMap American Sub 770 T=0.296 G=0.704
HapMap African Sub 692 T=0.701 G=0.299
HapMap Asian Sub 254 T=0.228 G=0.772
HapMap Europe Sub 176 T=0.415 G=0.585
Korean Genome Project KOREAN Study-wide 1832 T=0.2025 G=0.7975
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.307 G=0.693
Northern Sweden ACPOP Study-wide 600 T=0.353 G=0.647
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.371 G=0.629
SGDP_PRJ Global Study-wide 484 T=0.227 G=0.773
Qatari Global Study-wide 216 T=0.519 G=0.481
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.192 G=0.808
Siberian Global Study-wide 46 T=0.17 G=0.83
The Danish reference pan genome Danish Study-wide 40 T=0.23 G=0.78
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= G
GRCh38.p12 chr 3 NC_000003.12:g.120650728= NC_000003.12:g.120650728T>G
GRCh37.p13 chr 3 NC_000003.11:g.120369575= NC_000003.11:g.120369575T>G
HGD RefSeqGene NG_011957.1:g.36754= NG_011957.1:g.36754A>C
HGD transcript NM_000187.3:c.434+46= NM_000187.3:c.434+46A>C
HGD transcript NM_000187.4:c.434+46= NM_000187.4:c.434+46A>C
HGD transcript variant X1 XM_005247412.1:c.434+46= XM_005247412.1:c.434+46A>C
HGD transcript variant X1 XM_005247412.2:c.434+46= XM_005247412.2:c.434+46A>C
HGD transcript variant X2 XM_005247413.1:c.434+46= XM_005247413.1:c.434+46A>C
HGD transcript variant X2 XM_005247413.2:c.434+46= XM_005247413.2:c.434+46A>C
HGD transcript variant X3 XM_005247414.1:c.434+46= XM_005247414.1:c.434+46A>C
HGD transcript variant X5 XM_005247414.5:c.434+46= XM_005247414.5:c.434+46A>C
HGD transcript variant X4 XM_011512746.2:c.434+46= XM_011512746.2:c.434+46A>C
HGD transcript variant X3 XM_017006277.2:c.11+46= XM_017006277.2:c.11+46A>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#.

80 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss5004042 Aug 28, 2002 (107)
2 WI_SSAHASNP ss6439856 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10052357 Jul 11, 2003 (116)
4 PERLEGEN ss23258768 Sep 20, 2004 (123)
5 ABI ss41961133 Mar 15, 2006 (126)
6 AFFY ss66071643 Nov 30, 2006 (127)
7 PERLEGEN ss68873511 May 17, 2007 (127)
8 AFFY ss76002214 Dec 06, 2007 (131)
9 KRIBB_YJKIM ss81966145 Dec 15, 2007 (131)
10 BCMHGSC_JDW ss92257357 Mar 23, 2008 (130)
11 HUMANGENOME_JCVI ss99127253 Feb 05, 2009 (130)
12 BGI ss106293080 Feb 05, 2009 (130)
13 ENSEMBL ss133125250 Dec 01, 2009 (131)
14 GMI ss156111258 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162547572 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss167112806 Jul 04, 2010 (132)
17 AFFY ss170257727 Jul 04, 2010 (132)
18 BUSHMAN ss203091308 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss206026604 Jul 04, 2010 (132)
20 BL ss253439221 May 09, 2011 (134)
21 GMI ss277320349 May 04, 2012 (137)
22 GMI ss284734904 Apr 25, 2013 (138)
23 PJP ss292898990 May 09, 2011 (134)
24 1000GENOMES ss331004758 May 09, 2011 (134)
25 ILLUMINA ss479590577 May 04, 2012 (137)
26 ILLUMINA ss484444982 May 04, 2012 (137)
27 1000GENOMES ss489894694 May 04, 2012 (137)
28 ILLUMINA ss533114918 Sep 08, 2015 (146)
29 TISHKOFF ss556900129 Apr 25, 2013 (138)
30 SSMP ss650612020 Apr 25, 2013 (138)
31 NHLBI-ESP ss712547045 Apr 25, 2013 (138)
32 ILLUMINA ss779615112 Aug 21, 2014 (142)
33 ILLUMINA ss781019412 Aug 21, 2014 (142)
34 ILLUMINA ss835087389 Aug 21, 2014 (142)
35 EVA-GONL ss979083774 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1070777258 Aug 21, 2014 (142)
37 1000GENOMES ss1305859620 Aug 21, 2014 (142)
38 DDI ss1429564043 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1580152485 Apr 01, 2015 (144)
40 EVA_DECODE ss1588565992 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1608059391 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1651053424 Apr 01, 2015 (144)
43 EVA_EXAC ss1687158436 Apr 01, 2015 (144)
44 EVA_MGP ss1711029893 Apr 01, 2015 (144)
45 EVA_SVP ss1712606998 Apr 01, 2015 (144)
46 HAMMER_LAB ss1799930640 Sep 08, 2015 (146)
47 WEILL_CORNELL_DGM ss1922310105 Feb 12, 2016 (147)
48 GENOMED ss1969505770 Jul 19, 2016 (147)
49 JJLAB ss2021722860 Sep 14, 2016 (149)
50 USC_VALOUEV ss2149814995 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2255253615 Dec 20, 2016 (150)
52 TOPMED ss2422578046 Dec 20, 2016 (150)
53 SYSTEMSBIOZJU ss2625363276 Nov 08, 2017 (151)
54 ILLUMINA ss2634003241 Nov 08, 2017 (151)
55 GRF ss2705218305 Nov 08, 2017 (151)
56 GNOMAD ss2733990528 Nov 08, 2017 (151)
57 GNOMAD ss2747077602 Nov 08, 2017 (151)
58 GNOMAD ss2798280353 Nov 08, 2017 (151)
59 SWEGEN ss2993074404 Nov 08, 2017 (151)
60 BIOINF_KMB_FNS_UNIBA ss3024628245 Nov 08, 2017 (151)
61 CSHL ss3345231387 Nov 08, 2017 (151)
62 TOPMED ss3403599379 Nov 08, 2017 (151)
63 ILLUMINA ss3628759155 Oct 12, 2018 (152)
64 ILLUMINA ss3631946569 Oct 12, 2018 (152)
65 ILLUMINA ss3642277960 Oct 12, 2018 (152)
66 OMUKHERJEE_ADBS ss3646291545 Oct 12, 2018 (152)
67 URBANLAB ss3647510498 Oct 12, 2018 (152)
68 EGCUT_WGS ss3661001137 Jul 13, 2019 (153)
69 EVA_DECODE ss3710145464 Jul 13, 2019 (153)
70 ACPOP ss3730286714 Jul 13, 2019 (153)
71 EVA ss3760599345 Jul 13, 2019 (153)
72 KHV_HUMAN_GENOMES ss3803735622 Jul 13, 2019 (153)
73 EVA ss3823945437 Apr 25, 2020 (154)
74 EVA ss3825639975 Apr 25, 2020 (154)
75 EVA ss3828038305 Apr 25, 2020 (154)
76 EVA ss3837451350 Apr 25, 2020 (154)
77 EVA ss3842881621 Apr 25, 2020 (154)
78 SGDP_PRJ ss3856813944 Apr 25, 2020 (154)
79 KRGDB ss3902806483 Apr 25, 2020 (154)
80 KOGIC ss3952260907 Apr 25, 2020 (154)
81 1000Genomes NC_000003.11 - 120369575 Oct 12, 2018 (152)
82 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120369575 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000003.11 - 120369575 Oct 12, 2018 (152)
84 ExAC NC_000003.11 - 120369575 Oct 12, 2018 (152)
85 The Danish reference pan genome NC_000003.11 - 120369575 Apr 25, 2020 (154)
86 gnomAD - Genomes NC_000003.11 - 120369575 Jul 13, 2019 (153)
87 gnomAD - Exomes NC_000003.11 - 120369575 Jul 13, 2019 (153)
88 GO Exome Sequencing Project NC_000003.11 - 120369575 Oct 12, 2018 (152)
89 Genome of the Netherlands Release 5 NC_000003.11 - 120369575 Apr 25, 2020 (154)
90 HapMap NC_000003.12 - 120650728 Apr 25, 2020 (154)
91 KOREAN population from KRGDB NC_000003.11 - 120369575 Apr 25, 2020 (154)
92 Korean Genome Project NC_000003.12 - 120650728 Apr 25, 2020 (154)
93 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 120369575 Apr 25, 2020 (154)
94 Northern Sweden NC_000003.11 - 120369575 Jul 13, 2019 (153)
95 Qatari NC_000003.11 - 120369575 Apr 25, 2020 (154)
96 SGDP_PRJ NC_000003.11 - 120369575 Apr 25, 2020 (154)
97 Siberian NC_000003.11 - 120369575 Apr 25, 2020 (154)
98 TopMed NC_000003.12 - 120650728 Oct 12, 2018 (152)
99 UK 10K study - Twins NC_000003.11 - 120369575 Oct 12, 2018 (152)
100 A Vietnamese Genetic Variation Database NC_000003.11 - 120369575 Jul 13, 2019 (153)
101 dbGaP Population Frequency Project NC_000003.12 - 120650728 Apr 25, 2020 (154)
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)
rs55855947 Dec 02, 2009 (131)
rs61034929 Dec 02, 2009 (131)
rs61799356 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66071643, ss76002214, ss92257357, ss162547572, ss167112806, ss170257727, ss203091308, ss206026604, ss253439221, ss277320349, ss284734904, ss292898990, ss484444982, ss1588565992, ss1712606998 NC_000003.10:121852264:T:G NC_000003.12:120650727:T:G (self)
17112294, 9532283, 6739385, 7094364, 6317424, 46815877, 3076012, 403742, 4187801, 9983877, 145724, 3571579, 4352035, 8830924, 2331349, 9532283, 2077921, ss331004758, ss479590577, ss489894694, ss533114918, ss556900129, ss650612020, ss712547045, ss779615112, ss781019412, ss835087389, ss979083774, ss1070777258, ss1305859620, ss1429564043, ss1580152485, ss1608059391, ss1651053424, ss1687158436, ss1711029893, ss1799930640, ss1922310105, ss1969505770, ss2021722860, ss2149814995, ss2422578046, ss2625363276, ss2634003241, ss2705218305, ss2733990528, ss2747077602, ss2798280353, ss2993074404, ss3345231387, ss3628759155, ss3631946569, ss3642277960, ss3646291545, ss3661001137, ss3730286714, ss3760599345, ss3823945437, ss3825639975, ss3828038305, ss3837451350, ss3856813944, ss3902806483 NC_000003.11:120369574:T:G NC_000003.12:120650727:T:G (self)
2445498, 8638908, 261521301, 640078489, ss2255253615, ss3024628245, ss3403599379, ss3647510498, ss3710145464, ss3803735622, ss3842881621, ss3952260907 NC_000003.12:120650727:T:G NC_000003.12:120650727:T:G (self)
ss10052357 NT_005612.13:26768728:T:G NC_000003.12:120650727:T:G (self)
ss5004042, ss6439856, ss23258768, ss41961133, ss68873511, ss81966145, ss99127253, ss106293080, ss133125250, ss156111258 NT_005612.16:26864720:T:G NC_000003.12:120650727:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs3817627
PMID Title Author Year Journal
26960557 A Founder Effect for the HGD G360R Mutation in Italy: Implications for a Regional Screening of Alkaptonuria. Porfirio B et al. 2016 JIMD reports
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.post557+f76c771