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dbSNP Short Genetic Variations

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 153

Released July 9, 2019

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=0.34040 (85508/251200, GnomAD_exome)
T=0.40831 (51271/125568, TOPMED)
T=0.34351 (41672/121312, ExAC) (+ 8 more)
T=0.4116 (12899/31338, GnomAD)
T=0.4291 (5578/12998, GO-ESP)
T=0.397 (1986/5008, 1000G)
T=0.355 (1591/4480, Estonian)
T=0.326 (1255/3854, ALSPAC)
T=0.319 (1182/3708, TWINSUK)
T=0.35 (212/600, NorthernSweden)
T=0.19 (41/214, Vietnamese)
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. N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Intron Variant
HGD transcript variant X3 XM_017006277.2: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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251200 T=0.34040 G=0.65960
gnomAD - Exomes European Sub 135196 T=0.33807 G=0.66193
gnomAD - Exomes Asian Sub 48980 T=0.2617 G=0.7383
gnomAD - Exomes American Sub 34578 T=0.2869 G=0.7131
gnomAD - Exomes African Sub 16248 T=0.6161 G=0.3839
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=0.4857 G=0.5143
gnomAD - Exomes Other Sub 6130 T=0.353 G=0.647
TopMed Global Study-wide 125568 T=0.40831 G=0.59169
ExAC Global Study-wide 121312 T=0.34351 G=0.65649
ExAC Europe Sub 73306 T=0.3427 G=0.6573
ExAC Asian Sub 25130 T=0.2676 G=0.7324
ExAC American Sub 11570 T=0.2733 G=0.7267
ExAC African Sub 10398 T=0.6112 G=0.3888
ExAC Other Sub 908 T=0.34 G=0.66
gnomAD - Genomes Global Study-wide 31338 T=0.4116 G=0.5884
gnomAD - Genomes European Sub 18870 T=0.3454 G=0.6546
gnomAD - Genomes African Sub 8692 T=0.608 G=0.392
gnomAD - Genomes East Asian Sub 1554 T=0.187 G=0.813
gnomAD - Genomes Other Sub 1088 T=0.377 G=0.623
gnomAD - Genomes American Sub 846 T=0.29 G=0.71
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.51 G=0.49
GO Exome Sequencing Project Global Study-wide 12998 T=0.4291 G=0.5709
GO Exome Sequencing Project European American Sub 8592 T=0.341 G=0.659
GO Exome Sequencing Project African American Sub 4406 T=0.601 G=0.399
1000Genomes Global Study-wide 5008 T=0.397 G=0.603
1000Genomes African Sub 1322 T=0.686 G=0.314
1000Genomes East Asian Sub 1008 T=0.202 G=0.798
1000Genomes Europe Sub 1006 T=0.360 G=0.640
1000Genomes South Asian Sub 978 T=0.28 G=0.72
1000Genomes American Sub 694 T=0.35 G=0.65
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.355 G=0.645
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.326 G=0.674
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.319 G=0.681
Northern Sweden ACPOP Study-wide 600 T=0.35 G=0.65
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.19 G=0.81
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 Note
GRCh38.p12 chr 3 NC_000003.12:g.120650728= NC_000003.12:g.12065072...

NC_000003.12:g.120650728T>G

GRCh37.p13 chr 3 NC_000003.11:g.120369575= NC_000003.11:g.12036957...

NC_000003.11:g.120369575T>G

HGD RefSeqGene NG_011957.1:g.36754= NG_011957.1:g.36754A>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#.

72 SubSNP, 11 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 1000Genomes NC_000003.11 - 120369575 Oct 12, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120369575 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000003.11 - 120369575 Oct 12, 2018 (152)
76 ExAC NC_000003.11 - 120369575 Oct 12, 2018 (152)
77 gnomAD - Genomes NC_000003.11 - 120369575 Jul 13, 2019 (153)
78 gnomAD - Exomes NC_000003.11 - 120369575 Jul 13, 2019 (153)
79 GO Exome Sequencing Project NC_000003.11 - 120369575 Oct 12, 2018 (152)
80 Northern Sweden NC_000003.11 - 120369575 Jul 13, 2019 (153)
81 TopMed NC_000003.12 - 120650728 Oct 12, 2018 (152)
82 UK 10K study - Twins NC_000003.11 - 120369575 Oct 12, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000003.11 - 120369575 Jul 13, 2019 (153)
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, 46815877, 3076012, 403742, 3571579, 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 NC_000003.11:120369574:T:G NC_000003.12:120650727:T:G (self)
261521301, ss2255253615, ss3024628245, ss3403599379, ss3647510498, ss3710145464, ss3803735622 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

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.post246+3cda961