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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
chr3:120633005 (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
A=0.094132 (11820/125568, TOPMED)
A=0.09506 (2983/31380, GnomAD)
A=0.1192 (597/5008, 1000G) (+ 12 more)
A=0.1107 (496/4480, Estonian)
A=0.1155 (445/3854, ALSPAC)
A=0.1065 (395/3708, TWINSUK)
A=0.1853 (543/2930, KOREAN)
A=0.1015 (222/2188, ALFA Project)
A=0.110 (110/998, GoNL)
A=0.127 (76/600, NorthernSweden)
A=0.130 (28/216, Qatari)
A=0.243 (52/214, Vietnamese)
C=0.444 (71/160, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
C=0.44 (8/18, 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.120633005C>A
GRCh37.p13 chr 3 NC_000003.11:g.120351852C>A
HGD RefSeqGene NG_011957.1:g.54477G>T
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.1188+142G>T N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.963+142G…


N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.765+142G…


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 18890 C=0.90312 A=0.09688
European Sub 14286 C=0.89381 A=0.10619
African Sub 2946 C=0.9695 A=0.0305
African Others Sub 114 C=1.000 A=0.000
African American Sub 2832 C=0.9682 A=0.0318
Asian Sub 112 C=0.830 A=0.170
East Asian Sub 86 C=0.85 A=0.15
Other Asian Sub 26 C=0.77 A=0.23
Latin American 1 Sub 146 C=0.918 A=0.082
Latin American 2 Sub 610 C=0.831 A=0.169
South Asian Sub 98 C=0.86 A=0.14
Other Sub 692 C=0.892 A=0.108


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
TopMed Global Study-wide 125568 C=0.905868 A=0.094132
gnomAD - Genomes Global Study-wide 31380 C=0.90494 A=0.09506
gnomAD - Genomes European Sub 18900 C=0.88905 A=0.11095
gnomAD - Genomes African Sub 8706 C=0.9683 A=0.0317
gnomAD - Genomes East Asian Sub 1552 C=0.7964 A=0.2036
gnomAD - Genomes Other Sub 1086 C=0.8941 A=0.1059
gnomAD - Genomes American Sub 846 C=0.823 A=0.177
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.900 A=0.100
1000Genomes Global Study-wide 5008 C=0.8808 A=0.1192
1000Genomes African Sub 1322 C=0.9879 A=0.0121
1000Genomes East Asian Sub 1008 C=0.8185 A=0.1815
1000Genomes Europe Sub 1006 C=0.8966 A=0.1034
1000Genomes South Asian Sub 978 C=0.798 A=0.202
1000Genomes American Sub 694 C=0.862 A=0.138
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8893 A=0.1107
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8845 A=0.1155
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8935 A=0.1065
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8147 A=0.1853
ALFA Total Global 2188 C=0.8985 A=0.1015
ALFA European Sub 2072 C=0.8948 A=0.1052
ALFA African Sub 82 C=0.99 A=0.01
ALFA Other Sub 26 C=0.88 A=0.12
ALFA South Asian Sub 4 C=1.0 A=0.0
ALFA Asian Sub 4 C=1.0 A=0.0
ALFA Latin American 1 Sub 0 C=0 A=0
ALFA Latin American 2 Sub 0 C=0 A=0
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.890 A=0.110
Northern Sweden ACPOP Study-wide 600 C=0.873 A=0.127
Qatari Global Study-wide 216 C=0.870 A=0.130
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.757 A=0.243
SGDP_PRJ Global Study-wide 160 C=0.444 A=0.556
The Danish reference pan genome Danish Study-wide 40 C=0.97 A=0.03
Siberian Global Study-wide 18 C=0.44 A=0.56

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 C= A
GRCh38.p12 chr 3 NC_000003.12:g.120633005= NC_000003.12:g.120633005C>A
GRCh37.p13 chr 3 NC_000003.11:g.120351852= NC_000003.11:g.120351852C>A
HGD RefSeqGene NG_011957.1:g.54477= NG_011957.1:g.54477G>T
HGD transcript NM_000187.3:c.1188+142= NM_000187.3:c.1188+142G>T
HGD transcript NM_000187.4:c.1188+142= NM_000187.4:c.1188+142G>T
HGD transcript variant X1 XM_005247412.1:c.963+142= XM_005247412.1:c.963+142G>T
HGD transcript variant X1 XM_005247412.2:c.963+142= XM_005247412.2:c.963+142G>T
HGD transcript variant X3 XM_017006277.2:c.765+142= XM_017006277.2:c.765+142G>T

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#.

35 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss92257319 Mar 23, 2008 (129)
2 COMPLETE_GENOMICS ss167112656 Jul 04, 2010 (132)
3 BL ss253439105 May 09, 2011 (134)
4 GMI ss277320306 May 04, 2012 (137)
5 1000GENOMES ss331004601 May 09, 2011 (134)
6 SSMP ss650611960 Apr 25, 2013 (138)
7 EVA-GONL ss979083651 Aug 21, 2014 (142)
8 JMKIDD_LAB ss1070777172 Aug 21, 2014 (142)
9 1000GENOMES ss1305859126 Aug 21, 2014 (142)
10 DDI ss1429564014 Apr 01, 2015 (144)
11 EVA_GENOME_DK ss1580152432 Apr 01, 2015 (144)
12 EVA_DECODE ss1588565857 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1608059105 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1651053138 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1922309989 Feb 12, 2016 (147)
16 GENOMED ss1969505745 Jul 19, 2016 (147)
17 JJLAB ss2021722787 Sep 14, 2016 (149)
18 USC_VALOUEV ss2149814912 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2255252623 Dec 20, 2016 (150)
20 TOPMED ss2422577083 Dec 20, 2016 (150)
21 SYSTEMSBIOZJU ss2625363252 Nov 08, 2017 (151)
22 GRF ss2705218258 Nov 08, 2017 (151)
23 GNOMAD ss2798279072 Nov 08, 2017 (151)
24 SWEGEN ss2993074221 Nov 08, 2017 (151)
25 BIOINF_KMB_FNS_UNIBA ss3024628211 Nov 08, 2017 (151)
26 CSHL ss3345231322 Nov 08, 2017 (151)
27 TOPMED ss3403596372 Nov 08, 2017 (151)
28 EGCUT_WGS ss3661000923 Jul 13, 2019 (153)
29 EVA_DECODE ss3710145234 Jul 13, 2019 (153)
30 ACPOP ss3730286621 Jul 13, 2019 (153)
31 EVA ss3760599199 Jul 13, 2019 (153)
32 KHV_HUMAN_GENOMES ss3803735491 Jul 13, 2019 (153)
33 EVA ss3828038238 Apr 25, 2020 (154)
34 SGDP_PRJ ss3856813711 Apr 25, 2020 (154)
35 KRGDB ss3902806221 Apr 25, 2020 (154)
36 1000Genomes NC_000003.11 - 120351852 Oct 12, 2018 (152)
37 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120351852 Oct 12, 2018 (152)
38 Genetic variation in the Estonian population NC_000003.11 - 120351852 Oct 12, 2018 (152)
39 The Danish reference pan genome NC_000003.11 - 120351852 Apr 25, 2020 (154)
40 gnomAD - Genomes NC_000003.11 - 120351852 Jul 13, 2019 (153)
41 Genome of the Netherlands Release 5 NC_000003.11 - 120351852 Apr 25, 2020 (154)
42 KOREAN population from KRGDB NC_000003.11 - 120351852 Apr 25, 2020 (154)
43 Northern Sweden NC_000003.11 - 120351852 Jul 13, 2019 (153)
44 Qatari NC_000003.11 - 120351852 Apr 25, 2020 (154)
45 SGDP_PRJ NC_000003.11 - 120351852 Apr 25, 2020 (154)
46 Siberian NC_000003.11 - 120351852 Apr 25, 2020 (154)
47 TopMed NC_000003.12 - 120633005 Oct 12, 2018 (152)
48 UK 10K study - Twins NC_000003.11 - 120351852 Oct 12, 2018 (152)
49 A Vietnamese Genetic Variation Database NC_000003.11 - 120351852 Jul 13, 2019 (153)
50 dbGaP Population Frequency Project NC_000003.12 - 120633005 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
ss92257319, ss167112656, ss253439105, ss277320306, ss1588565857 NC_000003.10:121834541:C:A NC_000003.12:120633004:C:A (self)
17111788, 9531975, 6739171, 6317371, 46814588, 4187678, 9983615, 3571486, 4351919, 8830691, 2331266, 9531975, 2077854, ss331004601, ss650611960, ss979083651, ss1070777172, ss1305859126, ss1429564014, ss1580152432, ss1608059105, ss1651053138, ss1922309989, ss1969505745, ss2021722787, ss2149814912, ss2422577083, ss2625363252, ss2705218258, ss2798279072, ss2993074221, ss3345231322, ss3661000923, ss3730286621, ss3760599199, ss3828038238, ss3856813711, ss3902806221 NC_000003.11:120351851:C:A NC_000003.12:120633004:C:A (self)
261518768, 260474912, ss2255252623, ss3024628211, ss3403596372, ss3710145234, ss3803735491 NC_000003.12:120633004:C:A NC_000003.12:120633004:C:A (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 rs61799339


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