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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.


Current Build 154

Released April 21, 2020

Homo sapiens
chr3:120633096 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.034356 (8162/237572, GnomAD_exome)
C=0.065709 (8251/125568, TOPMED)
C=0.037156 (4046/108892, ExAC) (+ 16 more)
C=0.06686 (2098/31378, GnomAD)
C=0.07087 (921/12996, GO-ESP)
C=0.03965 (443/11174, ALFA Project)
C=0.0585 (293/5008, 1000G)
C=0.0478 (214/4480, Estonian)
C=0.0275 (106/3854, ALSPAC)
C=0.0272 (101/3708, TWINSUK)
C=0.020 (20/998, GoNL)
C=0.025 (15/600, NorthernSweden)
C=0.004 (2/534, MGP)
C=0.056 (12/216, Qatari)
C=0.009 (2/214, Vietnamese)
T=0.45 (19/42, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Intron Variant
0 citations
Genomic View
See rs on genome

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.120633096T>C
GRCh37.p13 chr 3 NC_000003.11:g.120351943T>C
HGD RefSeqGene NG_011957.1:g.54386A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.1188+51A>G N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.963+51A>G N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.765+51A>G N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Genic Downstream Transcript Variant

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 28250 T=0.94942 C=0.05058
European Sub 20396 T=0.96465 C=0.03535
African Sub 3578 T=0.8488 C=0.1512
African Others Sub 122 T=0.820 C=0.180
African American Sub 3456 T=0.8498 C=0.1502
Asian Sub 172 T=1.000 C=0.000
East Asian Sub 114 T=1.000 C=0.000
Other Asian Sub 58 T=1.00 C=0.00
Latin American 1 Sub 154 T=0.948 C=0.052
Latin American 2 Sub 616 T=0.977 C=0.023
South Asian Sub 98 T=0.97 C=0.03
Other Sub 3236 T=0.9561 C=0.0439


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 237572 T=0.965644 C=0.034356
gnomAD - Exomes European Sub 126530 T=0.967446 C=0.032554
gnomAD - Exomes Asian Sub 47274 T=0.99141 C=0.00859
gnomAD - Exomes American Sub 33004 T=0.98034 C=0.01966
gnomAD - Exomes African Sub 15204 T=0.84070 C=0.15930
gnomAD - Exomes Ashkenazi Jewish Sub 9722 T=0.9617 C=0.0383
gnomAD - Exomes Other Sub 5838 T=0.9668 C=0.0332
TopMed Global Study-wide 125568 T=0.934291 C=0.065709
ExAC Global Study-wide 108892 T=0.962844 C=0.037156
ExAC Europe Sub 66006 T=0.96738 C=0.03262
ExAC Asian Sub 23066 T=0.99124 C=0.00876
ExAC American Sub 9664 T=0.9832 C=0.0168
ExAC African Sub 9332 T=0.8403 C=0.1597
ExAC Other Sub 824 T=0.953 C=0.047
gnomAD - Genomes Global Study-wide 31378 T=0.93314 C=0.06686
gnomAD - Genomes European Sub 18894 T=0.96327 C=0.03673
gnomAD - Genomes African Sub 8698 T=0.8485 C=0.1515
gnomAD - Genomes East Asian Sub 1560 T=0.9994 C=0.0006
gnomAD - Genomes Other Sub 1088 T=0.9605 C=0.0395
gnomAD - Genomes American Sub 848 T=0.972 C=0.028
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.938 C=0.062
GO Exome Sequencing Project Global Study-wide 12996 T=0.92913 C=0.07087
GO Exome Sequencing Project European American Sub 8592 T=0.9708 C=0.0292
GO Exome Sequencing Project African American Sub 4404 T=0.8479 C=0.1521
ALFA Total Global 11174 T=0.96035 C=0.03965
ALFA European Sub 8132 T=0.9657 C=0.0343
ALFA Other Sub 2302 T=0.9605 C=0.0395
ALFA African Sub 676 T=0.893 C=0.107
ALFA Asian Sub 60 T=1.00 C=0.00
ALFA South Asian Sub 4 T=0.8 C=0.2
ALFA Latin American 1 Sub 0 T=0 C=0
ALFA Latin American 2 Sub 0 T=0 C=0
1000Genomes Global Study-wide 5008 T=0.9415 C=0.0585
1000Genomes African Sub 1322 T=0.8230 C=0.1770
1000Genomes East Asian Sub 1008 T=0.9990 C=0.0010
1000Genomes Europe Sub 1006 T=0.9732 C=0.0268
1000Genomes South Asian Sub 978 T=0.986 C=0.014
1000Genomes American Sub 694 T=0.976 C=0.024
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9522 C=0.0478
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9725 C=0.0275
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9728 C=0.0272
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.980 C=0.020
Northern Sweden ACPOP Study-wide 600 T=0.975 C=0.025
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.996 C=0.004
Qatari Global Study-wide 216 T=0.944 C=0.056
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.991 C=0.009
SGDP_PRJ Global Study-wide 42 T=0.45 C=0.55
The Danish reference pan genome Danish Study-wide 40 T=0.93 C=0.07
Siberian Global Study-wide 4 T=0.5 C=0.5

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= C
GRCh38.p12 chr 3 NC_000003.12:g.120633096= NC_000003.12:g.120633096T>C
GRCh37.p13 chr 3 NC_000003.11:g.120351943= NC_000003.11:g.120351943T>C
HGD RefSeqGene NG_011957.1:g.54386= NG_011957.1:g.54386A>G
HGD transcript NM_000187.3:c.1188+51= NM_000187.3:c.1188+51A>G
HGD transcript NM_000187.4:c.1188+51= NM_000187.4:c.1188+51A>G
HGD transcript variant X1 XM_005247412.1:c.963+51= XM_005247412.1:c.963+51A>G
HGD transcript variant X1 XM_005247412.2:c.963+51= XM_005247412.2:c.963+51A>G
HGD transcript variant X3 XM_017006277.2:c.765+51= XM_017006277.2:c.765+51A>G

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#.

38 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss203091185 Jul 04, 2010 (132)
2 GMI ss284734875 Apr 25, 2013 (138)
3 1000GENOMES ss331004602 May 09, 2011 (134)
4 ILLUMINA ss536056832 Sep 08, 2015 (146)
5 TISHKOFF ss556900074 Apr 25, 2013 (138)
6 NHLBI-ESP ss712546888 Apr 25, 2013 (138)
7 EVA-GONL ss979083652 Aug 21, 2014 (142)
8 JMKIDD_LAB ss1070777173 Aug 21, 2014 (142)
9 1000GENOMES ss1305859131 Aug 21, 2014 (142)
10 EVA_GENOME_DK ss1580152433 Apr 01, 2015 (144)
11 EVA_DECODE ss1588565858 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1608059106 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1651053139 Apr 01, 2015 (144)
14 EVA_EXAC ss1687158176 Apr 01, 2015 (144)
15 EVA_MGP ss1711029879 Apr 01, 2015 (144)
16 HAMMER_LAB ss1799930557 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1922309990 Feb 12, 2016 (147)
18 JJLAB ss2021722788 Sep 14, 2016 (149)
19 USC_VALOUEV ss2149814913 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2255252630 Dec 20, 2016 (150)
21 TOPMED ss2422577090 Dec 20, 2016 (150)
22 GNOMAD ss2733990117 Nov 08, 2017 (151)
23 GNOMAD ss2747077494 Nov 08, 2017 (151)
24 GNOMAD ss2798279081 Nov 08, 2017 (151)
25 SWEGEN ss2993074223 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3024628212 Nov 08, 2017 (151)
27 CSHL ss3345231323 Nov 08, 2017 (151)
28 TOPMED ss3403596393 Nov 08, 2017 (151)
29 ILLUMINA ss3628759113 Oct 12, 2018 (152)
30 OMUKHERJEE_ADBS ss3646291539 Oct 12, 2018 (152)
31 EGCUT_WGS ss3661000925 Jul 13, 2019 (153)
32 EVA_DECODE ss3710145235 Jul 13, 2019 (153)
33 ACPOP ss3730286622 Jul 13, 2019 (153)
34 EVA ss3760599200 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3803735492 Jul 13, 2019 (153)
36 EVA ss3823945380 Apr 25, 2020 (154)
37 EVA ss3828038239 Apr 25, 2020 (154)
38 SGDP_PRJ ss3856813712 Apr 25, 2020 (154)
39 1000Genomes NC_000003.11 - 120351943 Oct 12, 2018 (152)
40 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120351943 Oct 12, 2018 (152)
41 Genetic variation in the Estonian population NC_000003.11 - 120351943 Oct 12, 2018 (152)
42 ExAC NC_000003.11 - 120351943 Oct 12, 2018 (152)
43 The Danish reference pan genome NC_000003.11 - 120351943 Apr 25, 2020 (154)
44 gnomAD - Genomes NC_000003.11 - 120351943 Jul 13, 2019 (153)
45 gnomAD - Exomes NC_000003.11 - 120351943 Jul 13, 2019 (153)
46 GO Exome Sequencing Project NC_000003.11 - 120351943 Oct 12, 2018 (152)
47 Genome of the Netherlands Release 5 NC_000003.11 - 120351943 Apr 25, 2020 (154)
48 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 120351943 Apr 25, 2020 (154)
49 Northern Sweden NC_000003.11 - 120351943 Jul 13, 2019 (153)
50 Qatari NC_000003.11 - 120351943 Apr 25, 2020 (154)
51 SGDP_PRJ NC_000003.11 - 120351943 Apr 25, 2020 (154)
52 Siberian NC_000003.11 - 120351943 Apr 25, 2020 (154)
53 TopMed NC_000003.12 - 120633096 Oct 12, 2018 (152)
54 UK 10K study - Twins NC_000003.11 - 120351943 Oct 12, 2018 (152)
55 A Vietnamese Genetic Variation Database NC_000003.11 - 120351943 Jul 13, 2019 (153)
56 dbGaP Population Frequency Project NC_000003.12 - 120633096 Apr 25, 2020 (154)

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
ss203091185, ss284734875, ss1588565858 NC_000003.10:121834632:T:C NC_000003.12:120633095:T:C (self)
17111793, 9531976, 6739173, 7094089, 6317372, 46814597, 3075585, 403689, 4187679, 145711, 3571487, 4351920, 8830692, 2331267, 9531976, 2077855, ss331004602, ss536056832, ss556900074, ss712546888, ss979083652, ss1070777173, ss1305859131, ss1580152433, ss1608059106, ss1651053139, ss1687158176, ss1711029879, ss1799930557, ss1922309990, ss2021722788, ss2149814913, ss2422577090, ss2733990117, ss2747077494, ss2798279081, ss2993074223, ss3345231323, ss3628759113, ss3646291539, ss3661000925, ss3730286622, ss3760599200, ss3823945380, ss3828038239, ss3856813712 NC_000003.11:120351942:T:C NC_000003.12:120633095:T:C (self)
261518788, 246252137, ss2255252630, ss3024628212, ss3403596393, ss3710145235, ss3803735492 NC_000003.12:120633095:T:C NC_000003.12:120633095:T:C (self)

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

No publications for rs112229599


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