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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.

rs2733825

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120675757 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.15726 (39394/250502, GnomAD_exome)
A=0.14216 (17851/125568, TOPMED)
A=0.15809 (19116/120918, ExAC) (+ 8 more)
A=0.1408 (4416/31372, GnomAD)
A=0.1387 (1803/12998, GO-ESP)
A=0.111 (558/5008, 1000G)
A=0.178 (799/4480, Estonian)
A=0.156 (603/3854, ALSPAC)
A=0.153 (566/3708, TWINSUK)
A=0.20 (117/600, NorthernSweden)
A=0.09 (19/214, 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.120675757T>A
GRCh37.p13 chr 3 NC_000003.11:g.120394604T>A
HGD RefSeqGene NG_011957.1:g.11725A>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 250502 T=0.84274 A=0.15726
gnomAD - Exomes European Sub 134672 T=0.82531 A=0.17469
gnomAD - Exomes Asian Sub 48950 T=0.8792 A=0.1208
gnomAD - Exomes American Sub 34478 T=0.8445 A=0.1555
gnomAD - Exomes African Sub 16244 T=0.9336 A=0.0664
gnomAD - Exomes Ashkenazi Jewish Sub 10056 T=0.7566 A=0.2434
gnomAD - Exomes Other Sub 6102 T=0.825 A=0.175
TopMed Global Study-wide 125568 T=0.85784 A=0.14216
ExAC Global Study-wide 120918 T=0.84191 A=0.15809
ExAC Europe Sub 73092 T=0.8153 A=0.1847
ExAC Asian Sub 25076 T=0.8810 A=0.1190
ExAC American Sub 11452 T=0.8447 A=0.1553
ExAC African Sub 10394 T=0.9315 A=0.0685
ExAC Other Sub 904 T=0.84 A=0.16
gnomAD - Genomes Global Study-wide 31372 T=0.8592 A=0.1408
gnomAD - Genomes European Sub 18882 T=0.8295 A=0.1705
gnomAD - Genomes African Sub 8714 T=0.931 A=0.069
gnomAD - Genomes East Asian Sub 1554 T=0.847 A=0.153
gnomAD - Genomes Other Sub 1084 T=0.849 A=0.151
gnomAD - Genomes American Sub 848 T=0.85 A=0.15
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.76 A=0.24
GO Exome Sequencing Project Global Study-wide 12998 T=0.8613 A=0.1387
GO Exome Sequencing Project European American Sub 8592 T=0.828 A=0.172
GO Exome Sequencing Project African American Sub 4406 T=0.926 A=0.074
1000Genomes Global Study-wide 5008 T=0.889 A=0.111
1000Genomes African Sub 1322 T=0.955 A=0.045
1000Genomes East Asian Sub 1008 T=0.862 A=0.138
1000Genomes Europe Sub 1006 T=0.801 A=0.199
1000Genomes South Asian Sub 978 T=0.93 A=0.07
1000Genomes American Sub 694 T=0.87 A=0.13
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.822 A=0.178
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.844 A=0.156
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.847 A=0.153
Northern Sweden ACPOP Study-wide 600 T=0.81 A=0.20
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.91 A=0.09
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= A Note
GRCh38.p12 chr 3 NC_000003.12:g.120675757= NC_000003.12:g.12067575...

NC_000003.12:g.120675757T>A

GRCh37.p13 chr 3 NC_000003.11:g.120394604= NC_000003.11:g.12039460...

NC_000003.11:g.120394604T>A

HGD RefSeqGene NG_011957.1:g.11725= NG_011957.1:g.11725A>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#.

46 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3859292 Sep 28, 2001 (100)
2 PERLEGEN ss23899066 Sep 20, 2004 (123)
3 BGI ss103978175 Dec 01, 2009 (131)
4 GMI ss156111586 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss162547913 Jul 04, 2010 (132)
6 COMPLETE_GENOMICS ss164111063 Jul 04, 2010 (132)
7 COMPLETE_GENOMICS ss167113216 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss206099712 Jul 04, 2010 (132)
9 GMI ss277320445 May 04, 2012 (137)
10 1000GENOMES ss331005044 May 09, 2011 (134)
11 1000GENOMES ss489894734 May 04, 2012 (137)
12 SSMP ss650612163 Apr 25, 2013 (138)
13 NHLBI-ESP ss712547093 Apr 25, 2013 (138)
14 EVA-GONL ss979084000 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1070777438 Aug 21, 2014 (142)
16 1000GENOMES ss1305860342 Aug 21, 2014 (142)
17 DDI ss1429564140 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1580152607 Apr 01, 2015 (144)
19 EVA_DECODE ss1588566213 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1608059813 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1651053846 Apr 01, 2015 (144)
22 EVA_EXAC ss1687158595 Apr 01, 2015 (144)
23 EVA_MGP ss1711029913 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1922310317 Feb 12, 2016 (147)
25 JJLAB ss2021723001 Sep 14, 2016 (149)
26 USC_VALOUEV ss2149815135 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2255255122 Dec 20, 2016 (150)
28 TOPMED ss2422579515 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2625363341 Nov 08, 2017 (151)
30 GRF ss2705218425 Nov 08, 2017 (151)
31 GNOMAD ss2733990731 Nov 08, 2017 (151)
32 GNOMAD ss2747077675 Nov 08, 2017 (151)
33 GNOMAD ss2798282213 Nov 08, 2017 (151)
34 SWEGEN ss2993074691 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3024628341 Nov 08, 2017 (151)
36 CSHL ss3345231519 Nov 08, 2017 (151)
37 TOPMED ss3403603760 Nov 08, 2017 (151)
38 OMUKHERJEE_ADBS ss3646291556 Oct 12, 2018 (152)
39 EGCUT_WGS ss3661001476 Jul 13, 2019 (153)
40 EVA_DECODE ss3710145809 Jul 13, 2019 (153)
41 ACPOP ss3730286898 Jul 13, 2019 (153)
42 EVA ss3760599582 Jul 13, 2019 (153)
43 PACBIO ss3784443353 Jul 13, 2019 (153)
44 PACBIO ss3789940801 Jul 13, 2019 (153)
45 PACBIO ss3794815236 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3803735870 Jul 13, 2019 (153)
47 1000Genomes NC_000003.11 - 120394604 Oct 12, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120394604 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000003.11 - 120394604 Oct 12, 2018 (152)
50 ExAC NC_000003.11 - 120394604 Oct 12, 2018 (152)
51 gnomAD - Genomes NC_000003.11 - 120394604 Jul 13, 2019 (153)
52 gnomAD - Exomes NC_000003.11 - 120394604 Jul 13, 2019 (153)
53 GO Exome Sequencing Project NC_000003.11 - 120394604 Oct 12, 2018 (152)
54 Northern Sweden NC_000003.11 - 120394604 Jul 13, 2019 (153)
55 TopMed NC_000003.12 - 120675757 Oct 12, 2018 (152)
56 UK 10K study - Twins NC_000003.11 - 120394604 Oct 12, 2018 (152)
57 A Vietnamese Genetic Variation Database NC_000003.11 - 120394604 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)
rs16831533 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss162547913, ss164111063, ss167113216, ss206099712, ss277320445, ss1588566213 NC_000003.10:121877293:T:A NC_000003.12:120675756:T:A (self)
17113041, 9532749, 6739724, 7094531, 46817764, 3076238, 403793, 3571763, 9532749, 2078050, ss331005044, ss489894734, ss650612163, ss712547093, ss979084000, ss1070777438, ss1305860342, ss1429564140, ss1580152607, ss1608059813, ss1651053846, ss1687158595, ss1711029913, ss1922310317, ss2021723001, ss2149815135, ss2422579515, ss2625363341, ss2705218425, ss2733990731, ss2747077675, ss2798282213, ss2993074691, ss3345231519, ss3646291556, ss3661001476, ss3730286898, ss3760599582, ss3784443353, ss3789940801, ss3794815236 NC_000003.11:120394603:T:A NC_000003.12:120675756:T:A (self)
261525019, ss2255255122, ss3024628341, ss3403603760, ss3710145809, ss3803735870 NC_000003.12:120675756:T:A NC_000003.12:120675756:T:A (self)
ss3859292, ss23899066, ss103978175, ss156111586 NT_005612.16:26889749:T:A NC_000003.12:120675756:T: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 rs2733825
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