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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.

rs199560759

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:37426624 (GRCh38.p14) 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
A=0.000332 (88/264690, TOPMED)
A=0.000302 (76/251446, GnomAD_exome)
A=0.000271 (54/199282, ALFA) (+ 13 more)
A=0.000242 (34/140224, GnomAD)
A=0.000223 (27/121256, ExAC)
A=0.00050 (39/78700, PAGE_STUDY)
A=0.00042 (12/28258, 14KJPN)
A=0.00036 (6/16760, 8.3KJPN)
A=0.00038 (5/13006, GO-ESP)
A=0.0005 (3/6404, 1000G_30x)
A=0.0006 (3/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.001 (1/998, GoNL)
A=0.002 (1/600, NorthernSweden)
A=0.004 (2/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GRHPR : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 215694 G=0.999740 A=0.000260
European Sub 180080 G=0.999706 A=0.000294
African Sub 9792 G=0.9999 A=0.0001
African Others Sub 360 G=1.000 A=0.000
African American Sub 9432 G=0.9999 A=0.0001
Asian Sub 6350 G=1.0000 A=0.0000
East Asian Sub 4502 G=1.0000 A=0.0000
Other Asian Sub 1848 G=1.0000 A=0.0000
Latin American 1 Sub 796 G=1.000 A=0.000
Latin American 2 Sub 968 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 17428 G=0.99989 A=0.00011


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999668 A=0.000332
gnomAD - Exomes Global Study-wide 251446 G=0.999698 A=0.000302
gnomAD - Exomes European Sub 135382 G=0.999705 A=0.000295
gnomAD - Exomes Asian Sub 49008 G=0.99969 A=0.00031
gnomAD - Exomes American Sub 34590 G=0.99957 A=0.00043
gnomAD - Exomes African Sub 16252 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6136 G=0.9990 A=0.0010
Allele Frequency Aggregator Total Global 199282 G=0.999729 A=0.000271
Allele Frequency Aggregator European Sub 169940 G=0.999700 A=0.000300
Allele Frequency Aggregator Other Sub 15994 G=0.99987 A=0.00013
Allele Frequency Aggregator Asian Sub 6350 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 4954 G=0.9998 A=0.0002
Allele Frequency Aggregator Latin American 2 Sub 968 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140224 G=0.999758 A=0.000242
gnomAD - Genomes European Sub 75952 G=0.99983 A=0.00017
gnomAD - Genomes African Sub 42018 G=0.99988 A=0.00012
gnomAD - Genomes American Sub 13648 G=0.99897 A=0.00103
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2150 G=0.9995 A=0.0005
ExAC Global Study-wide 121256 G=0.999777 A=0.000223
ExAC Europe Sub 73270 G=0.99975 A=0.00025
ExAC Asian Sub 25144 G=0.99980 A=0.00020
ExAC American Sub 11568 G=0.99965 A=0.00035
ExAC African Sub 10368 G=1.00000 A=0.00000
ExAC Other Sub 906 G=1.000 A=0.000
The PAGE Study Global Study-wide 78700 G=0.99950 A=0.00050
The PAGE Study AfricanAmerican Sub 32516 G=0.99994 A=0.00006
The PAGE Study Mexican Sub 10808 G=0.99907 A=0.00093
The PAGE Study Asian Sub 8318 G=0.9998 A=0.0002
The PAGE Study PuertoRican Sub 7918 G=0.9990 A=0.0010
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=0.9981 A=0.0019
The PAGE Study Dominican Sub 3828 G=0.9982 A=0.0018
The PAGE Study CentralAmerican Sub 2450 G=0.9996 A=0.0004
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99958 A=0.00042
8.3KJPN JAPANESE Study-wide 16760 G=0.99964 A=0.00036
GO Exome Sequencing Project Global Study-wide 13006 G=0.99962 A=0.00038
GO Exome Sequencing Project European American Sub 8600 G=0.9994 A=0.0006
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
1000Genomes_30x Global Study-wide 6404 G=0.9995 A=0.0005
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=0.999 A=0.001
1000Genomes Global Study-wide 5008 G=0.9994 A=0.0006
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9980 A=0.0020
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.999 A=0.001
Northern Sweden ACPOP Study-wide 600 G=0.998 A=0.002
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.996 A=0.004
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.p14 chr 9 NC_000009.12:g.37426624G>A
GRCh37.p13 chr 9 NC_000009.11:g.37426621G>A
GRHPR RefSeqGene NG_008135.1:g.8915G>A
Gene: GRHPR, glyoxylate and hydroxypyruvate reductase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GRHPR transcript NM_012203.2:c.374G>A R [CGG] > Q [CAG] Coding Sequence Variant
glyoxylate reductase/hydroxypyruvate reductase NP_036335.1:p.Arg125Gln R (Arg) > Q (Gln) Missense Variant
GRHPR transcript variant X7 XM_005251631.2:c.84-1860G…

XM_005251631.2:c.84-1860G>A

N/A Intron Variant
GRHPR transcript variant X6 XM_047424084.1:c.84-1860G…

XM_047424084.1:c.84-1860G>A

N/A Intron Variant
GRHPR transcript variant X8 XM_017015323.3:c. N/A Genic Upstream Transcript Variant
GRHPR transcript variant X9 XM_047424085.1:c. N/A Genic Upstream Transcript Variant
GRHPR transcript variant X1 XM_024447716.2:c.647G>A R [CGG] > Q [CAG] Coding Sequence Variant
glyoxylate reductase/hydroxypyruvate reductase isoform X1 XP_024303484.1:p.Arg216Gln R (Arg) > Q (Gln) Missense Variant
GRHPR transcript variant X3 XM_017015320.3:c.374G>A R [CGG] > Q [CAG] Coding Sequence Variant
glyoxylate reductase/hydroxypyruvate reductase isoform X2 XP_016870809.1:p.Arg125Gln R (Arg) > Q (Gln) Missense Variant
GRHPR transcript variant X4 XM_017015321.3:c.374G>A R [CGG] > Q [CAG] Coding Sequence Variant
glyoxylate reductase/hydroxypyruvate reductase isoform X3 XP_016870810.1:p.Arg125Gln R (Arg) > Q (Gln) Missense Variant
GRHPR transcript variant X2 XR_002956828.2:n.662G>A N/A Non Coding Transcript Variant
GRHPR transcript variant X5 XR_007061375.1:n.429G>A N/A Non Coding Transcript 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.

Allele: A (allele ID: 902067 )
ClinVar Accession Disease Names Clinical Significance
RCV001169807.3 Primary hyperoxaluria, type II Uncertain-Significance
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
GRCh38.p14 chr 9 NC_000009.12:g.37426624= NC_000009.12:g.37426624G>A
GRCh37.p13 chr 9 NC_000009.11:g.37426621= NC_000009.11:g.37426621G>A
GRHPR RefSeqGene NG_008135.1:g.8915= NG_008135.1:g.8915G>A
GRHPR transcript NM_012203.2:c.374= NM_012203.2:c.374G>A
GRHPR transcript NM_012203.1:c.374= NM_012203.1:c.374G>A
GRHPR transcript variant X4 XM_017015321.3:c.374= XM_017015321.3:c.374G>A
GRHPR transcript variant X7 XM_017015321.2:c.374= XM_017015321.2:c.374G>A
GRHPR transcript variant X2 XM_017015321.1:c.374= XM_017015321.1:c.374G>A
GRHPR transcript variant X3 XM_017015320.3:c.374= XM_017015320.3:c.374G>A
GRHPR transcript variant X6 XM_017015320.2:c.374= XM_017015320.2:c.374G>A
GRHPR transcript variant X1 XM_017015320.1:c.374= XM_017015320.1:c.374G>A
GRHPR transcript variant X1 XM_024447716.2:c.647= XM_024447716.2:c.647G>A
GRHPR transcript variant X1 XM_024447716.1:c.647= XM_024447716.1:c.647G>A
GRHPR transcript variant X2 XR_002956828.2:n.662= XR_002956828.2:n.662G>A
GRHPR transcript variant X2 XR_002956828.1:n.662= XR_002956828.1:n.662G>A
GRHPR transcript variant X5 XR_007061375.1:n.429= XR_007061375.1:n.429G>A
glyoxylate reductase/hydroxypyruvate reductase NP_036335.1:p.Arg125= NP_036335.1:p.Arg125Gln
glyoxylate reductase/hydroxypyruvate reductase isoform X3 XP_016870810.1:p.Arg125= XP_016870810.1:p.Arg125Gln
glyoxylate reductase/hydroxypyruvate reductase isoform X2 XP_016870809.1:p.Arg125= XP_016870809.1:p.Arg125Gln
glyoxylate reductase/hydroxypyruvate reductase isoform X1 XP_024303484.1:p.Arg216= XP_024303484.1:p.Arg216Gln
GRHPR transcript variant X10 XM_005251631.1:c.84-1860= XM_005251631.1:c.84-1860G>A
GRHPR transcript variant X7 XM_005251631.2:c.84-1860= XM_005251631.2:c.84-1860G>A
GRHPR transcript variant X6 XM_047424084.1:c.84-1860= XM_047424084.1:c.84-1860G>A
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#.

52 SubSNP, 16 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488905956 May 04, 2012 (137)
2 EXOME_CHIP ss491422635 May 04, 2012 (137)
3 CLINSEQ_SNP ss491935498 May 04, 2012 (137)
4 NHLBI-ESP ss712886561 Apr 25, 2013 (138)
5 ILLUMINA ss780876765 Sep 08, 2015 (146)
6 ILLUMINA ss783562262 Sep 08, 2015 (146)
7 EVA-GONL ss986539050 Aug 21, 2014 (142)
8 1000GENOMES ss1333770291 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1622705223 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1665699256 Apr 01, 2015 (144)
11 EVA_EXAC ss1689488058 Apr 01, 2015 (144)
12 EVA_MGP ss1711221710 Apr 01, 2015 (144)
13 ILLUMINA ss1752777579 Sep 08, 2015 (146)
14 ILLUMINA ss1917836371 Feb 12, 2016 (147)
15 ILLUMINA ss1946258114 Feb 12, 2016 (147)
16 ILLUMINA ss1959182190 Feb 12, 2016 (147)
17 HUMAN_LONGEVITY ss2311174055 Dec 20, 2016 (150)
18 GNOMAD ss2737608370 Nov 08, 2017 (151)
19 GNOMAD ss2748185439 Nov 08, 2017 (151)
20 GNOMAD ss2877872615 Nov 08, 2017 (151)
21 AFFY ss2985461728 Nov 08, 2017 (151)
22 ILLUMINA ss3022927139 Nov 08, 2017 (151)
23 ILLUMINA ss3630261359 Oct 12, 2018 (152)
24 ILLUMINA ss3635212911 Oct 12, 2018 (152)
25 ILLUMINA ss3640920201 Oct 12, 2018 (152)
26 ILLUMINA ss3644991440 Oct 12, 2018 (152)
27 ILLUMINA ss3653479432 Oct 12, 2018 (152)
28 ILLUMINA ss3654225788 Oct 12, 2018 (152)
29 ILLUMINA ss3726610540 Jul 13, 2019 (153)
30 ACPOP ss3736498323 Jul 13, 2019 (153)
31 ILLUMINA ss3744588914 Jul 13, 2019 (153)
32 ILLUMINA ss3745512824 Jul 13, 2019 (153)
33 EVA ss3769181470 Jul 13, 2019 (153)
34 PAGE_CC ss3771499427 Jul 13, 2019 (153)
35 ILLUMINA ss3773004861 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3812337799 Jul 13, 2019 (153)
37 EVA ss3824430122 Apr 26, 2020 (154)
38 TOPMED ss4820292202 Apr 26, 2021 (155)
39 TOMMO_GENOMICS ss5193046925 Apr 26, 2021 (155)
40 EVA ss5237458930 Apr 26, 2021 (155)
41 1000G_HIGH_COVERAGE ss5280545422 Oct 13, 2022 (156)
42 EVA ss5315401347 Oct 13, 2022 (156)
43 EVA ss5387403945 Oct 13, 2022 (156)
44 HUGCELL_USP ss5476744930 Oct 13, 2022 (156)
45 1000G_HIGH_COVERAGE ss5572720105 Oct 13, 2022 (156)
46 SANFORD_IMAGENETICS ss5624719009 Oct 13, 2022 (156)
47 SANFORD_IMAGENETICS ss5647342987 Oct 13, 2022 (156)
48 TOMMO_GENOMICS ss5736372007 Oct 13, 2022 (156)
49 EVA ss5848205448 Oct 13, 2022 (156)
50 EVA ss5916384743 Oct 13, 2022 (156)
51 EVA ss5976625047 Oct 13, 2022 (156)
52 EVA ss5979892504 Oct 13, 2022 (156)
53 1000Genomes NC_000009.11 - 37426621 Oct 12, 2018 (152)
54 1000Genomes_30x NC_000009.12 - 37426624 Oct 13, 2022 (156)
55 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 37426621 Oct 12, 2018 (152)
56 ExAC NC_000009.11 - 37426621 Oct 12, 2018 (152)
57 gnomAD - Genomes NC_000009.12 - 37426624 Apr 26, 2021 (155)
58 gnomAD - Exomes NC_000009.11 - 37426621 Jul 13, 2019 (153)
59 GO Exome Sequencing Project NC_000009.11 - 37426621 Oct 12, 2018 (152)
60 Genome of the Netherlands Release 5 NC_000009.11 - 37426621 Apr 26, 2020 (154)
61 Medical Genome Project healthy controls from Spanish population NC_000009.11 - 37426621 Apr 26, 2020 (154)
62 Northern Sweden NC_000009.11 - 37426621 Jul 13, 2019 (153)
63 The PAGE Study NC_000009.12 - 37426624 Jul 13, 2019 (153)
64 8.3KJPN NC_000009.11 - 37426621 Apr 26, 2021 (155)
65 14KJPN NC_000009.12 - 37426624 Oct 13, 2022 (156)
66 TopMed NC_000009.12 - 37426624 Apr 26, 2021 (155)
67 UK 10K study - Twins NC_000009.11 - 37426621 Oct 12, 2018 (152)
68 ALFA NC_000009.12 - 37426624 Apr 26, 2021 (155)
69 ClinVar RCV001169807.3 Oct 13, 2022 (156)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491935498 NC_000009.10:37416620:G:A NC_000009.12:37426623:G:A (self)
46026298, 25602767, 9610823, 6792462, 887914, 11421091, 337470, 9783188, 51016232, 25602767, ss488905956, ss491422635, ss712886561, ss780876765, ss783562262, ss986539050, ss1333770291, ss1622705223, ss1665699256, ss1689488058, ss1711221710, ss1752777579, ss1917836371, ss1946258114, ss1959182190, ss2737608370, ss2748185439, ss2877872615, ss2985461728, ss3022927139, ss3630261359, ss3635212911, ss3640920201, ss3644991440, ss3653479432, ss3654225788, ss3736498323, ss3744588914, ss3745512824, ss3769181470, ss3773004861, ss3824430122, ss5193046925, ss5237458930, ss5315401347, ss5387403945, ss5624719009, ss5647342987, ss5848205448, ss5976625047, ss5979892504 NC_000009.11:37426620:G:A NC_000009.12:37426623:G:A (self)
RCV001169807.3, 60246040, 324386381, 720896, 70209111, 657669763, 487462404, ss2311174055, ss3726610540, ss3771499427, ss3812337799, ss4820292202, ss5280545422, ss5476744930, ss5572720105, ss5736372007, ss5916384743 NC_000009.12:37426623:G:A NC_000009.12:37426623: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.

No publications for rs199560759

Help

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.post761+d5e8e07