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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.

rs2551607

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120652567 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.10385 (26000/250372, GnomAD_exome)
G=0.17396 (21844/125568, TOPMED)
G=0.11090 (13403/120862, ExAC) (+ 8 more)
G=0.1636 (5123/31306, GnomAD)
G=0.1905 (2476/12998, GO-ESP)
G=0.169 (846/5008, 1000G)
G=0.073 (327/4480, Estonian)
G=0.105 (406/3854, ALSPAC)
G=0.107 (396/3708, TWINSUK)
G=0.03 (16/616, Vietnamese)
G=0.10 (58/600, NorthernSweden)
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.120652567G>A
GRCh37.p13 chr 3 NC_000003.11:g.120371414G>A
HGD RefSeqGene NG_011957.1:g.34915C>T
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 250372 G=0.10385 A=0.89615
gnomAD - Exomes European Sub 134632 G=0.08929 A=0.91071
gnomAD - Exomes Asian Sub 48842 G=0.0799 A=0.9201
gnomAD - Exomes American Sub 34526 G=0.0659 A=0.9341
gnomAD - Exomes African Sub 16210 G=0.3754 A=0.6246
gnomAD - Exomes Ashkenazi Jewish Sub 10050 G=0.1088 A=0.8912
gnomAD - Exomes Other Sub 6112 G=0.102 A=0.898
TopMed Global Study-wide 125568 G=0.17396 A=0.82604
ExAC Global Study-wide 120862 G=0.11090 A=0.88910
ExAC Europe Sub 73050 G=0.0907 A=0.9093
ExAC Asian Sub 25012 G=0.0834 A=0.9166
ExAC American Sub 11526 G=0.0681 A=0.9319
ExAC African Sub 10374 G=0.3683 A=0.6317
ExAC Other Sub 900 G=0.09 A=0.91
gnomAD - Genomes Global Study-wide 31306 G=0.1636 A=0.8364
gnomAD - Genomes European Sub 18882 G=0.0854 A=0.9146
gnomAD - Genomes African Sub 8644 G=0.378 A=0.622
gnomAD - Genomes East Asian Sub 1556 G=0.022 A=0.978
gnomAD - Genomes Other Sub 1086 G=0.101 A=0.899
gnomAD - Genomes American Sub 848 G=0.07 A=0.93
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.12 A=0.88
GO Exome Sequencing Project Global Study-wide 12998 G=0.1905 A=0.8095
GO Exome Sequencing Project European American Sub 8592 G=0.103 A=0.897
GO Exome Sequencing Project African American Sub 4406 G=0.361 A=0.639
1000Genomes Global Study-wide 5008 G=0.169 A=0.831
1000Genomes African Sub 1322 G=0.427 A=0.573
1000Genomes East Asian Sub 1008 G=0.015 A=0.985
1000Genomes Europe Sub 1006 G=0.079 A=0.921
1000Genomes South Asian Sub 978 G=0.12 A=0.88
1000Genomes American Sub 694 G=0.10 A=0.90
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.073 A=0.927
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.105 A=0.895
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.107 A=0.893
A Vietnamese Genetic Variation Database Global Study-wide 616 G=0.03 A=0.97
Northern Sweden ACPOP Study-wide 600 G=0.10 A=0.90
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 G= A Note
GRCh38.p12 chr 3 NC_000003.12:g.120652567= NC_000003.12:g.12065256...

NC_000003.12:g.120652567G>A

GRCh37.p13 chr 3 NC_000003.11:g.120371414= NC_000003.11:g.12037141...

NC_000003.11:g.120371414G>A

HGD RefSeqGene NG_011957.1:g.34915= NG_011957.1:g.34915C>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, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3580995 Sep 28, 2001 (100)
2 CGAP-GAI ss4323087 Jan 04, 2002 (102)
3 BGI ss5593553 Dec 12, 2002 (110)
4 WI_SSAHASNP ss6439682 Feb 20, 2003 (111)
5 ABI ss41978280 Mar 13, 2006 (126)
6 BCMHGSC_JDW ss92257361 Mar 23, 2008 (130)
7 HUMANGENOME_JCVI ss99127255 Feb 04, 2009 (130)
8 BGI ss106293082 Feb 04, 2009 (130)
9 ENSEMBL ss135530520 Dec 01, 2009 (131)
10 GMI ss156111273 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss162547584 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss167112822 Jul 04, 2010 (132)
13 BUSHMAN ss203091323 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss205999431 Jul 04, 2010 (132)
15 BL ss253439232 May 09, 2011 (134)
16 GMI ss277320354 May 04, 2012 (137)
17 GMI ss284734910 Apr 25, 2013 (138)
18 PJP ss292898993 May 09, 2011 (134)
19 1000GENOMES ss331004775 May 09, 2011 (134)
20 ILLUMINA ss484175363 May 04, 2012 (137)
21 ILLUMINA ss484444990 May 04, 2012 (137)
22 1000GENOMES ss489894702 May 04, 2012 (137)
23 ILLUMINA ss536364247 Sep 08, 2015 (146)
24 TISHKOFF ss556900136 Apr 25, 2013 (138)
25 SSMP ss650612028 Apr 25, 2013 (138)
26 NHLBI-ESP ss712547053 Apr 25, 2013 (138)
27 ILLUMINA ss780555091 Sep 08, 2015 (146)
28 ILLUMINA ss782533630 Sep 08, 2015 (146)
29 ILLUMINA ss836047245 Sep 08, 2015 (146)
30 JMKIDD_LAB ss974449390 Aug 21, 2014 (142)
31 EVA-GONL ss979083790 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1067454150 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1070777272 Aug 21, 2014 (142)
34 1000GENOMES ss1305859676 Aug 21, 2014 (142)
35 DDI ss1429564046 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1580152493 Apr 01, 2015 (144)
37 EVA_FINRISK ss1584029644 Apr 01, 2015 (144)
38 EVA_DECODE ss1588566010 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1608059419 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1651053452 Apr 01, 2015 (144)
41 EVA_EXAC ss1687158484 Apr 01, 2015 (144)
42 EVA_MGP ss1711029898 Apr 01, 2015 (144)
43 HAMMER_LAB ss1799930650 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1922310115 Feb 12, 2016 (147)
45 GENOMED ss1969505773 Jul 19, 2016 (147)
46 JJLAB ss2021722870 Sep 14, 2016 (149)
47 USC_VALOUEV ss2149815004 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2255253724 Dec 20, 2016 (150)
49 TOPMED ss2422578138 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2625363279 Nov 08, 2017 (151)
51 ILLUMINA ss2634003245 Nov 08, 2017 (151)
52 GRF ss2705218310 Nov 08, 2017 (151)
53 GNOMAD ss2733990578 Nov 08, 2017 (151)
54 GNOMAD ss2747077620 Nov 08, 2017 (151)
55 GNOMAD ss2798280483 Nov 08, 2017 (151)
56 SWEGEN ss2993074423 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3024628249 Nov 08, 2017 (151)
58 CSHL ss3345231394 Nov 08, 2017 (151)
59 TOPMED ss3403599694 Nov 08, 2017 (151)
60 ILLUMINA ss3628759162 Oct 12, 2018 (152)
61 ILLUMINA ss3631946573 Oct 12, 2018 (152)
62 ILLUMINA ss3642277964 Oct 12, 2018 (152)
63 OMUKHERJEE_ADBS ss3646291548 Oct 12, 2018 (152)
64 URBANLAB ss3647510500 Oct 12, 2018 (152)
65 EGCUT_WGS ss3661001152 Jul 13, 2019 (153)
66 EVA_DECODE ss3710145481 Jul 13, 2019 (153)
67 ACPOP ss3730286725 Jul 13, 2019 (153)
68 EVA ss3760599357 Jul 13, 2019 (153)
69 PACBIO ss3784443281 Jul 13, 2019 (153)
70 PACBIO ss3789940732 Jul 13, 2019 (153)
71 PACBIO ss3794815167 Jul 13, 2019 (153)
72 KHV_HUMAN_GENOMES ss3803735637 Jul 13, 2019 (153)
73 1000Genomes NC_000003.11 - 120371414 Oct 12, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120371414 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000003.11 - 120371414 Oct 12, 2018 (152)
76 ExAC NC_000003.11 - 120371414 Oct 12, 2018 (152)
77 gnomAD - Genomes NC_000003.11 - 120371414 Jul 13, 2019 (153)
78 gnomAD - Exomes NC_000003.11 - 120371414 Jul 13, 2019 (153)
79 GO Exome Sequencing Project NC_000003.11 - 120371414 Oct 12, 2018 (152)
80 Northern Sweden NC_000003.11 - 120371414 Jul 13, 2019 (153)
81 TopMed NC_000003.12 - 120652567 Oct 12, 2018 (152)
82 UK 10K study - Twins NC_000003.11 - 120371414 Oct 12, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000003.11 - 120371414 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)
rs61799358 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss92257361, ss162547584, ss167112822, ss203091323, ss205999431, ss253439232, ss277320354, ss284734910, ss292898993, ss484444990, ss1588566010 NC_000003.10:121854103:G:A NC_000003.12:120652566:G:A (self)
17112350, 9532312, 6739400, 7094415, 46816003, 3076075, 403755, 3571590, 9532312, 2077935, ss331004775, ss484175363, ss489894702, ss536364247, ss556900136, ss650612028, ss712547053, ss780555091, ss782533630, ss836047245, ss974449390, ss979083790, ss1067454150, ss1070777272, ss1305859676, ss1429564046, ss1580152493, ss1584029644, ss1608059419, ss1651053452, ss1687158484, ss1711029898, ss1799930650, ss1922310115, ss1969505773, ss2021722870, ss2149815004, ss2422578138, ss2625363279, ss2634003245, ss2705218310, ss2733990578, ss2747077620, ss2798280483, ss2993074423, ss3345231394, ss3628759162, ss3631946573, ss3642277964, ss3646291548, ss3661001152, ss3730286725, ss3760599357, ss3784443281, ss3789940732, ss3794815167 NC_000003.11:120371413:G:A NC_000003.12:120652566:G:A (self)
261521585, ss2255253724, ss3024628249, ss3403599694, ss3647510500, ss3710145481, ss3803735637 NC_000003.12:120652566:G:A NC_000003.12:120652566:G:A (self)
ss3580995, ss4323087, ss5593553, ss6439682, ss41978280, ss99127255, ss106293082, ss135530520, ss156111273 NT_005612.16:26866559:G:A NC_000003.12:120652566:G:A (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 rs2551607
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