Name: rs533425
Published: September 21, 2022
License: Open Access

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.

rs533425

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:34447777 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.252325 (66788/264690, TOPMED)
A=0.290559 (40719/140140, GnomAD)
A=0.33561 (17234/51352, ALFA) (+ 16 more)
A=0.02505 (708/28258, 14KJPN)
A=0.02560 (429/16758, 8.3KJPN)
A=0.1849 (1184/6404, 1000G_30x)
A=0.1853 (928/5008, 1000G)
A=0.4451 (1994/4480, Estonian)
A=0.4128 (1591/3854, ALSPAC)
A=0.4121 (1528/3708, TWINSUK)
A=0.0297 (87/2930, KOREAN)
A=0.1607 (304/1892, HapMap)
A=0.396 (395/998, GoNL)
A=0.495 (297/600, NorthernSweden)
A=0.119 (63/528, SGDP_PRJ)
A=0.208 (45/216, Qatari)
A=0.033 (7/212, Vietnamese)
A=0.19 (9/48, Siberian)
A=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CAT : Intron Variant
Publications: 2 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	51352	A=0.33561	G=0.66439
European	Sub	36010	A=0.39833	G=0.60167
African	Sub	6074	A=0.0813	G=0.9187
African Others	Sub	214	A=0.009	G=0.991
African American	Sub	5860	A=0.0840	G=0.9160
Asian	Sub	444	A=0.043	G=0.957
East Asian	Sub	378	A=0.042	G=0.958
Other Asian	Sub	66	A=0.05	G=0.95
Latin American 1	Sub	584	A=0.276	G=0.724
Latin American 2	Sub	4782	A=0.2039	G=0.7961
South Asian	Sub	162	A=0.321	G=0.679
Other	Sub	3296	A=0.3607	G=0.6393

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
TopMed	Global	Study-wide	264690	A=0.252325	G=0.747675
gnomAD - Genomes	Global	Study-wide	140140	A=0.290559	G=0.709441
gnomAD - Genomes	European	Sub	75836	A=0.42721	G=0.57279
gnomAD - Genomes	African	Sub	42038	A=0.08464	G=0.91536
gnomAD - Genomes	American	Sub	13656	A=0.22862	G=0.77138
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2945	G=0.7055
gnomAD - Genomes	East Asian	Sub	3132	A=0.0335	G=0.9665
gnomAD - Genomes	Other	Sub	2154	A=0.2586	G=0.7414
Allele Frequency Aggregator	Total	Global	51352	A=0.33561	G=0.66439
Allele Frequency Aggregator	European	Sub	36010	A=0.39833	G=0.60167
Allele Frequency Aggregator	African	Sub	6074	A=0.0813	G=0.9187
Allele Frequency Aggregator	Latin American 2	Sub	4782	A=0.2039	G=0.7961
Allele Frequency Aggregator	Other	Sub	3296	A=0.3607	G=0.6393
Allele Frequency Aggregator	Latin American 1	Sub	584	A=0.276	G=0.724
Allele Frequency Aggregator	Asian	Sub	444	A=0.043	G=0.957
Allele Frequency Aggregator	South Asian	Sub	162	A=0.321	G=0.679
14KJPN	JAPANESE	Study-wide	28258	A=0.02505	G=0.97495
8.3KJPN	JAPANESE	Study-wide	16758	A=0.02560	G=0.97440
1000Genomes_30x	Global	Study-wide	6404	A=0.1849	G=0.8151
1000Genomes_30x	African	Sub	1786	A=0.0274	G=0.9726
1000Genomes_30x	Europe	Sub	1266	A=0.4107	G=0.5893
1000Genomes_30x	South Asian	Sub	1202	A=0.2953	G=0.7047
1000Genomes_30x	East Asian	Sub	1170	A=0.0308	G=0.9692
1000Genomes_30x	American	Sub	980	A=0.229	G=0.771
1000Genomes	Global	Study-wide	5008	A=0.1853	G=0.8147
1000Genomes	African	Sub	1322	A=0.0325	G=0.9675
1000Genomes	East Asian	Sub	1008	A=0.0298	G=0.9702
1000Genomes	Europe	Sub	1006	A=0.4036	G=0.5964
1000Genomes	South Asian	Sub	978	A=0.298	G=0.702
1000Genomes	American	Sub	694	A=0.228	G=0.772
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.4451	G=0.5549
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.4128	G=0.5872
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.4121	G=0.5879
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.0297	C=0.0000, G=0.9703, T=0.0000
HapMap	Global	Study-wide	1892	A=0.1607	G=0.8393
HapMap	American	Sub	770	A=0.242	G=0.758
HapMap	African	Sub	692	A=0.074	G=0.926
HapMap	Asian	Sub	254	A=0.031	G=0.969
HapMap	Europe	Sub	176	A=0.335	G=0.665
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.396	G=0.604
Northern Sweden	ACPOP	Study-wide	600	A=0.495	G=0.505
SGDP_PRJ	Global	Study-wide	528	A=0.119	G=0.881
Qatari	Global	Study-wide	216	A=0.208	G=0.792
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.033	G=0.967
Siberian	Global	Study-wide	48	A=0.19	G=0.81
The Danish reference pan genome	Danish	Study-wide	40	A=0.38	G=0.62

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 11	NC_000011.10:g.34447777A>C
GRCh38.p14 chr 11	NC_000011.10:g.34447777A>G
GRCh38.p14 chr 11	NC_000011.10:g.34447777A>T
GRCh37.p13 chr 11	NC_000011.9:g.34469324A>C
GRCh37.p13 chr 11	NC_000011.9:g.34469324A>G
GRCh37.p13 chr 11	NC_000011.9:g.34469324A>T
CAT RefSeqGene	NG_013339.2:g.13853A>C
CAT RefSeqGene	NG_013339.2:g.13853A>G
CAT RefSeqGene	NG_013339.2:g.13853A>T

Gene: CAT, catalase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAT transcript	NM_001752.4:c.67-1415A>C	N/A	Intron 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

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	A=	C	G	T
GRCh38.p14 chr 11	NC_000011.10:g.34447777=	NC_000011.10:g.34447777A>C	NC_000011.10:g.34447777A>G	NC_000011.10:g.34447777A>T
GRCh37.p13 chr 11	NC_000011.9:g.34469324=	NC_000011.9:g.34469324A>C	NC_000011.9:g.34469324A>G	NC_000011.9:g.34469324A>T
CAT RefSeqGene	NG_013339.2:g.13853=	NG_013339.2:g.13853A>C	NG_013339.2:g.13853A>G	NG_013339.2:g.13853A>T
CAT transcript	NM_001752.3:c.67-1415=	NM_001752.3:c.67-1415A>C	NM_001752.3:c.67-1415A>G	NM_001752.3:c.67-1415A>T
CAT transcript	NM_001752.4:c.67-1415=	NM_001752.4:c.67-1415A>C	NM_001752.4:c.67-1415A>G	NM_001752.4:c.67-1415A>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#.

92 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss703999	Aug 11, 2000 (83)
2	KWOK	ss1247784	Oct 04, 2000 (86)
3	KWOK	ss1963828	Oct 18, 2000 (87)
4	SC_JCM	ss2593119	Nov 08, 2000 (89)
5	SC_JCM	ss4197086	Nov 05, 2001 (101)
6	WI_SSAHASNP	ss12129186	Jul 11, 2003 (116)
7	CSHL-HAPMAP	ss17440164	Feb 27, 2004 (120)
8	SSAHASNP	ss20755237	Apr 05, 2004 (121)
9	PGA-UW-FHCRC	ss28527597	Dec 02, 2004 (126)
10	ABI	ss39895593	Mar 11, 2006 (126)
11	ILLUMINA	ss75231955	Dec 06, 2007 (129)
12	HGSV	ss77482622	Dec 06, 2007 (129)
13	HGSV	ss85503934	Dec 14, 2007 (130)
14	BGI	ss106734966	Feb 04, 2009 (130)
15	1000GENOMES	ss110307283	Jan 24, 2009 (130)
16	1000GENOMES	ss114452860	Jan 25, 2009 (130)
17	KRIBB_YJKIM	ss119357121	Dec 01, 2009 (131)
18	ILLUMINA-UK	ss119787270	Dec 01, 2009 (131)
19	ENSEMBL	ss131992221	Dec 01, 2009 (131)
20	ILLUMINA	ss160740510	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss168180508	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss169608096	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss170778501	Jul 04, 2010 (132)
24	ILLUMINA	ss173915291	Jul 04, 2010 (132)
25	BUSHMAN	ss202575217	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss207592373	Jul 04, 2010 (132)
27	1000GENOMES	ss225185500	Jul 14, 2010 (132)
28	1000GENOMES	ss235515349	Jul 15, 2010 (132)
29	1000GENOMES	ss242156183	Jul 15, 2010 (132)
30	BL	ss255036024	May 09, 2011 (134)
31	GMI	ss280954030	May 04, 2012 (137)
32	GMI	ss286351713	Apr 25, 2013 (138)
33	PJP	ss291217395	May 09, 2011 (134)
34	ILLUMINA	ss482151308	Sep 08, 2015 (146)
35	ILLUMINA	ss537308379	Sep 08, 2015 (146)
36	TISHKOFF	ss562493268	Apr 25, 2013 (138)
37	SSMP	ss657984781	Apr 25, 2013 (138)
38	EVA-GONL	ss988393689	Aug 21, 2014 (142)
39	JMKIDD_LAB	ss1077637561	Aug 21, 2014 (142)
40	1000GENOMES	ss1340791502	Aug 21, 2014 (142)
41	DDI	ss1426596614	Apr 01, 2015 (144)
42	EVA_GENOME_DK	ss1575638431	Apr 01, 2015 (144)
43	EVA_DECODE	ss1598070177	Apr 01, 2015 (144)
44	EVA_UK10K_ALSPAC	ss1626347364	Apr 01, 2015 (144)
45	EVA_UK10K_TWINSUK	ss1669341397	Apr 01, 2015 (144)
46	EVA_SVP	ss1713247348	Apr 01, 2015 (144)
47	HAMMER_LAB	ss1806770306	Sep 08, 2015 (146)
48	WEILL_CORNELL_DGM	ss1931752095	Feb 12, 2016 (147)
49	GENOMED	ss1967337885	Jul 19, 2016 (147)
50	JJLAB	ss2026623170	Sep 14, 2016 (149)
51	USC_VALOUEV	ss2154912670	Dec 20, 2016 (150)
52	HUMAN_LONGEVITY	ss2181579168	Dec 20, 2016 (150)
53	SYSTEMSBIOZJU	ss2627785348	Nov 08, 2017 (151)
54	GRF	ss2699192481	Nov 08, 2017 (151)
55	GNOMAD	ss2898235034	Nov 08, 2017 (151)
56	SWEGEN	ss3007872526	Nov 08, 2017 (151)
57	BIOINF_KMB_FNS_UNIBA	ss3027110508	Nov 08, 2017 (151)
58	CSHL	ss3349536641	Nov 08, 2017 (151)
59	ILLUMINA	ss3626637057	Oct 12, 2018 (152)
60	ILLUMINA	ss3636133702	Oct 12, 2018 (152)
61	ILLUMINA	ss3637900833	Oct 12, 2018 (152)
62	ILLUMINA	ss3642899816	Oct 12, 2018 (152)
63	URBANLAB	ss3649578262	Oct 12, 2018 (152)
64	EGCUT_WGS	ss3675278668	Jul 13, 2019 (153)
65	EVA_DECODE	ss3691549789	Jul 13, 2019 (153)
66	ACPOP	ss3738074708	Jul 13, 2019 (153)
67	EVA	ss3749150196	Jul 13, 2019 (153)
68	PACBIO	ss3786920493	Jul 13, 2019 (153)
69	PACBIO	ss3792067318	Jul 13, 2019 (153)
70	PACBIO	ss3796949467	Jul 13, 2019 (153)
71	KHV_HUMAN_GENOMES	ss3814499392	Jul 13, 2019 (153)
72	EVA	ss3832570216	Apr 26, 2020 (154)
73	EVA	ss3839836293	Apr 26, 2020 (154)
74	EVA	ss3845313928	Apr 26, 2020 (154)
75	SGDP_PRJ	ss3876001870	Apr 26, 2020 (154)
76	KRGDB	ss3924258790	Apr 26, 2020 (154)
77	EVA	ss4017532522	Apr 26, 2021 (155)
78	TOPMED	ss4881103555	Apr 26, 2021 (155)
79	TOMMO_GENOMICS	ss5201438356	Apr 26, 2021 (155)
80	1000G_HIGH_COVERAGE	ss5286989456	Oct 16, 2022 (156)
81	EVA	ss5398815223	Oct 16, 2022 (156)
82	HUGCELL_USP	ss5482232283	Oct 16, 2022 (156)
83	EVA	ss5510316698	Oct 16, 2022 (156)
84	1000G_HIGH_COVERAGE	ss5582422718	Oct 16, 2022 (156)
85	SANFORD_IMAGENETICS	ss5650976467	Oct 16, 2022 (156)
86	TOMMO_GENOMICS	ss5748406754	Oct 16, 2022 (156)
87	YY_MCH	ss5812277545	Oct 16, 2022 (156)
88	EVA	ss5836494669	Oct 16, 2022 (156)
89	EVA	ss5849933630	Oct 16, 2022 (156)
90	EVA	ss5919505632	Oct 16, 2022 (156)
91	EVA	ss5942291111	Oct 16, 2022 (156)
92	EVA	ss5980670440	Oct 16, 2022 (156)
93	1000Genomes	NC_000011.9 - 34469324	Oct 12, 2018 (152)
94	1000Genomes_30x	NC_000011.10 - 34447777	Oct 16, 2022 (156)
95	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 34469324	Oct 12, 2018 (152)
96	Genetic variation in the Estonian population	NC_000011.9 - 34469324	Oct 12, 2018 (152)
97	The Danish reference pan genome	NC_000011.9 - 34469324	Apr 26, 2020 (154)
98	gnomAD - Genomes	NC_000011.10 - 34447777	Apr 26, 2021 (155)
99	Genome of the Netherlands Release 5	NC_000011.9 - 34469324	Apr 26, 2020 (154)
100	HapMap	NC_000011.10 - 34447777	Apr 26, 2020 (154)
101	KOREAN population from KRGDB	NC_000011.9 - 34469324	Apr 26, 2020 (154)
102	Northern Sweden	NC_000011.9 - 34469324	Jul 13, 2019 (153)
103	Qatari	NC_000011.9 - 34469324	Apr 26, 2020 (154)
104	SGDP_PRJ	NC_000011.9 - 34469324	Apr 26, 2020 (154)
105	Siberian	NC_000011.9 - 34469324	Apr 26, 2020 (154)
106	8.3KJPN	NC_000011.9 - 34469324	Apr 26, 2021 (155)
107	14KJPN	NC_000011.10 - 34447777	Oct 16, 2022 (156)
108	TopMed	NC_000011.10 - 34447777	Apr 26, 2021 (155)
109	UK 10K study - Twins	NC_000011.9 - 34469324	Oct 12, 2018 (152)
110	A Vietnamese Genetic Variation Database	NC_000011.9 - 34469324	Jul 13, 2019 (153)
111	ALFA	NC_000011.10 - 34447777	Apr 26, 2021 (155)

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)
rs17881617	Mar 11, 2006 (126)
rs57814824	May 24, 2008 (130)
rs386598377	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
31436184, ss3924258790	NC_000011.9:34469323:A:C	NC_000011.10:34447776:A:C	(self)
ss77482622, ss85503934, ss110307283, ss114452860, ss119787270, ss168180508, ss169608096, ss170778501, ss202575217, ss207592373, ss255036024, ss280954030, ss286351713, ss291217395, ss1598070177, ss1713247348, ss3642899816	NC_000011.8:34425899:A:G	NC_000011.10:34447776:A:G	(self)
53299173, 29609704, 21016916, 2517197, 13208083, 31436184, 11359573, 13794025, 28018850, 7429024, 59407663, 29609704, 6576815, ss225185500, ss235515349, ss242156183, ss482151308, ss537308379, ss562493268, ss657984781, ss988393689, ss1077637561, ss1340791502, ss1426596614, ss1575638431, ss1626347364, ss1669341397, ss1806770306, ss1931752095, ss1967337885, ss2026623170, ss2154912670, ss2627785348, ss2699192481, ss2898235034, ss3007872526, ss3349536641, ss3626637057, ss3636133702, ss3637900833, ss3675278668, ss3738074708, ss3749150196, ss3786920493, ss3792067318, ss3796949467, ss3832570216, ss3839836293, ss3876001870, ss3924258790, ss4017532522, ss5201438356, ss5398815223, ss5510316698, ss5650976467, ss5836494669, ss5942291111, ss5980670440	NC_000011.9:34469323:A:G	NC_000011.10:34447776:A:G	(self)
69948653, 376231584, 588164, 82243858, 96649211, 133379972, ss2181579168, ss3027110508, ss3649578262, ss3691549789, ss3814499392, ss3845313928, ss4881103555, ss5286989456, ss5482232283, ss5582422718, ss5748406754, ss5812277545, ss5849933630, ss5919505632	NC_000011.10:34447776:A:G	NC_000011.10:34447776:A:G	(self)
ss12129186	NT_009237.15:25870427:A:G	NC_000011.10:34447776:A:G	(self)
ss17440164, ss20755237	NT_009237.16:33233263:A:G	NC_000011.10:34447776:A:G	(self)
ss703999, ss1247784, ss1963828, ss2593119, ss4197086, ss28527597, ss39895593, ss75231955, ss106734966, ss119357121, ss131992221, ss160740510, ss173915291	NT_009237.18:34409323:A:G	NC_000011.10:34447776:A:G	(self)
31436184, ss3924258790	NC_000011.9:34469323:A:T	NC_000011.10:34447776:A:T	(self)

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

2 citations for rs533425

PMID	Title	Author	Year	Journal
22824134	Polymorphism in glutamate cysteine ligase catalytic subunit (GCLC) is associated with sulfamethoxazole-induced hypersensitivity in HIV/AIDS patients.	Wang D et al.	2012	BMC medical genomics
25463281	Association between maternal micronutrient status, oxidative stress, and common genetic variants in antioxidant enzymes at 15 weeks׳ gestation in nulliparous women who subsequently develop preeclampsia.	Mistry HD et al.	2015	Free radical biology & medicine

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs533425