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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.

rs6446261

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:49357420 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00944 (1185/125568, TOPMED)
T=0.0090 (283/31366, GnomAD)
T=0.0078 (91/11604, GO-ESP) (+ 1 more)
T=0.013 (63/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPX1 : Missense Variant
Publications
0 citations
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.49357420C>G
GRCh38.p12 chr 3 NC_000003.12:g.49357420C>T
GRCh37.p13 chr 3 NC_000003.11:g.49394853C>G
GRCh37.p13 chr 3 NC_000003.11:g.49394853C>T
RHOA RefSeqGene NG_051308.1:g.59678G>C
RHOA RefSeqGene NG_051308.1:g.59678G>A
GPX1 RefSeqGene NG_012264.1:g.5939G>C
GPX1 RefSeqGene NG_012264.1:g.5939G>A
Gene: GPX1, glutathione peroxidase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPX1 transcript variant 3 NM_001329502.2:c. N/A 3 Prime UTR Variant
GPX1 transcript variant 2 NM_201397.3:c. N/A 3 Prime UTR Variant
GPX1 transcript variant 4 NM_001329503.2:c. N/A 3 Prime UTR Variant
GPX1 transcript variant 5 NM_001329455.1:c.442G>C A [GCC] > P [CCC] Coding Sequence Variant
glutathione peroxidase 1 isoform 5 NP_001316384.1:p.Ala148Pro A (Ala) > P (Pro) Missense Variant
GPX1 transcript variant 5 NM_001329455.1:c.442G>A A [GCC] > T [ACC] Coding Sequence Variant
glutathione peroxidase 1 isoform 5 NP_001316384.1:p.Ala148Thr A (Ala) > T (Thr) Missense Variant
GPX1 transcript variant 1 NM_000581.4:c.580G>C A [GCC] > P [CCC] Coding Sequence Variant
glutathione peroxidase 1 isoform 1 NP_000572.2:p.Ala194Pro A (Ala) > P (Pro) Missense Variant
GPX1 transcript variant 1 NM_000581.4:c.580G>A A [GCC] > T [ACC] Coding Sequence Variant
glutathione peroxidase 1 isoform 1 NP_000572.2:p.Ala194Thr A (Ala) > T (Thr) Missense 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.99056 T=0.00944
gnomAD - Genomes Global Study-wide 31366 C=0.9910 T=0.0090
gnomAD - Genomes European Sub 18882 C=0.9997 T=0.0003
gnomAD - Genomes African Sub 8700 C=0.969 T=0.031
gnomAD - Genomes East Asian Sub 1558 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 C=0.997 T=0.003
gnomAD - Genomes American Sub 848 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 11604 C=0.9922 T=0.0078
GO Exome Sequencing Project European American Sub 7974 C=1.000 T=0.000
GO Exome Sequencing Project African American Sub 3630 C=0.976 T=0.024
1000Genomes Global Study-wide 5008 C=0.987 T=0.013
1000Genomes African Sub 1322 C=0.957 T=0.043
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.999 T=0.001
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
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 C= G T Note
GRCh38.p12 chr 3 NC_000003.12:g.49...

NC_000003.12:g.49357420=

NC_000003.12:g.49...

NC_000003.12:g.49357420C>G

NC_000003.12:g.49...

NC_000003.12:g.49357420C>T

GRCh37.p13 chr 3 NC_000003.11:g.49...

NC_000003.11:g.49394853=

NC_000003.11:g.49...

NC_000003.11:g.49394853C>G

NC_000003.11:g.49...

NC_000003.11:g.49394853C>T

RHOA RefSeqGene NG_051308.1:g.59678= NG_051308.1:g.596...

NG_051308.1:g.59678G>C

NG_051308.1:g.596...

NG_051308.1:g.59678G>A

GPX1 RefSeqGene NG_012264.1:g.5939= NG_012264.1:g.593...

NG_012264.1:g.5939G>C

NG_012264.1:g.593...

NG_012264.1:g.5939G>A

GPX1 transcript variant 1 NM_000581.4:c.580= NM_000581.4:c.580G>C NM_000581.4:c.580G>A
GPX1 transcript variant 1 NM_000581.3:c.580= NM_000581.3:c.580G>C NM_000581.3:c.580G>A
GPX1 transcript variant 1 NM_000581.2:c.580= NM_000581.2:c.580G>C NM_000581.2:c.580G>A
GPX1 transcript variant 2 NM_201397.3:c.*562= NM_201397.3:c.*56...

NM_201397.3:c.*562G>C

NM_201397.3:c.*56...

NM_201397.3:c.*562G>A

GPX1 transcript variant 2 NM_201397.2:c.*562= NM_201397.2:c.*56...

NM_201397.2:c.*562G>C

NM_201397.2:c.*56...

NM_201397.2:c.*562G>A

GPX1 transcript variant 2 NM_201397.1:c.*562= NM_201397.1:c.*56...

NM_201397.1:c.*562G>C

NM_201397.1:c.*56...

NM_201397.1:c.*562G>A

GPX1 transcript variant 3 NM_001329502.2:c....

NM_001329502.2:c.*406=

NM_001329502.2:c....

NM_001329502.2:c.*406G>C

NM_001329502.2:c....

NM_001329502.2:c.*406G>A

GPX1 transcript variant 3 NM_001329502.1:c....

NM_001329502.1:c.*406=

NM_001329502.1:c....

NM_001329502.1:c.*406G>C

NM_001329502.1:c....

NM_001329502.1:c.*406G>A

GPX1 transcript variant 4 NM_001329503.2:c....

NM_001329503.2:c.*86=

NM_001329503.2:c....

NM_001329503.2:c.*86G>C

NM_001329503.2:c....

NM_001329503.2:c.*86G>A

GPX1 transcript variant 4 NM_001329503.1:c....

NM_001329503.1:c.*86=

NM_001329503.1:c....

NM_001329503.1:c.*86G>C

NM_001329503.1:c....

NM_001329503.1:c.*86G>A

GPX1 transcript variant 5 NM_001329455.1:c....

NM_001329455.1:c.442=

NM_001329455.1:c....

NM_001329455.1:c.442G>C

NM_001329455.1:c....

NM_001329455.1:c.442G>A

glutathione peroxidase 1 isoform 1 NP_000572.2:p.Ala...

NP_000572.2:p.Ala194=

NP_000572.2:p.Ala...

NP_000572.2:p.Ala194Pro

NP_000572.2:p.Ala...

NP_000572.2:p.Ala194Thr

glutathione peroxidase 1 isoform 5 NP_001316384.1:p....

NP_001316384.1:p.Ala148=

NP_001316384.1:p....

NP_001316384.1:p.Ala148Pro

NP_001316384.1:p....

NP_001316384.1:p.Ala148Thr

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#.

29 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10070307 Jul 11, 2003 (116)
2 WI_SSAHASNP ss11582997 Jul 11, 2003 (116)
3 EGP_SNPS ss12568571 Aug 26, 2003 (117)
4 SNP500CANCER ss105435061 Feb 05, 2009 (130)
5 ILLUMINA ss244304909 Jul 04, 2010 (142)
6 1000GENOMES ss330677167 May 09, 2011 (134)
7 1000GENOMES ss489878320 May 04, 2012 (137)
8 EXOME_CHIP ss491339808 May 04, 2012 (137)
9 ILLUMINA ss535054662 Sep 08, 2015 (146)
10 TISHKOFF ss556599609 Apr 25, 2013 (138)
11 NHLBI-ESP ss712519614 Apr 25, 2013 (138)
12 1000GENOMES ss1303895772 Aug 21, 2014 (142)
13 EVA_EXAC ss1687007066 Apr 01, 2015 (144)
14 EVA_EXAC ss1687007067 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1921806686 Feb 12, 2016 (147)
16 ILLUMINA ss1946082635 Feb 12, 2016 (147)
17 HUMAN_LONGEVITY ss2251344215 Dec 20, 2016 (150)
18 TOPMED ss2418421427 Dec 20, 2016 (150)
19 ILLUMINA ss2710972163 Nov 08, 2017 (151)
20 GNOMAD ss2733753808 Nov 08, 2017 (151)
21 GNOMAD ss2747008362 Nov 08, 2017 (151)
22 GNOMAD ss2792646713 Nov 08, 2017 (151)
23 AFFY ss2985256239 Nov 08, 2017 (151)
24 AFFY ss2985876680 Nov 08, 2017 (151)
25 SWEGEN ss2992271617 Nov 08, 2017 (151)
26 TOPMED ss3389831761 Nov 08, 2017 (151)
27 ILLUMINA ss3628654106 Oct 12, 2018 (152)
28 ILLUMINA ss3654024593 Oct 12, 2018 (152)
29 EVA_DECODE ss3709179306 Jul 13, 2019 (153)
30 1000Genomes NC_000003.11 - 49394853 Oct 12, 2018 (152)
31 ExAC

Submission ignored due to conflicting rows:
Row 6931399 (NC_000003.11:49394852:C:C 114847/115320, NC_000003.11:49394852:C:T 473/115320)
Row 6931400 (NC_000003.11:49394852:C:C 115319/115320, NC_000003.11:49394852:C:G 1/115320)

- Oct 12, 2018 (152)
32 ExAC

Submission ignored due to conflicting rows:
Row 6931399 (NC_000003.11:49394852:C:C 114847/115320, NC_000003.11:49394852:C:T 473/115320)
Row 6931400 (NC_000003.11:49394852:C:C 115319/115320, NC_000003.11:49394852:C:G 1/115320)

- Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000003.11 - 49394853 Jul 13, 2019 (153)
34 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2832621 (NC_000003.11:49394852:C:C 245163/245164, NC_000003.11:49394852:C:G 1/245164)
Row 2832622 (NC_000003.11:49394852:C:C 244278/245164, NC_000003.11:49394852:C:T 886/245164)

- Jul 13, 2019 (153)
35 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2832621 (NC_000003.11:49394852:C:C 245163/245164, NC_000003.11:49394852:C:G 1/245164)
Row 2832622 (NC_000003.11:49394852:C:C 244278/245164, NC_000003.11:49394852:C:T 886/245164)

- Jul 13, 2019 (153)
36 GO Exome Sequencing Project NC_000003.11 - 49394853 Oct 12, 2018 (152)
37 TopMed NC_000003.12 - 49357420 Oct 12, 2018 (152)
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)
rs113960317 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1687007067, ss2733753808 NC_000003.11:49394852:C:G NC_000003.12:49357419:C:G (self)
15080190, 41216609, 371885, ss330677167, ss489878320, ss491339808, ss535054662, ss556599609, ss712519614, ss1303895772, ss1687007066, ss1921806686, ss1946082635, ss2418421427, ss2710972163, ss2733753808, ss2747008362, ss2792646713, ss2985256239, ss2985876680, ss2992271617, ss3628654106, ss3654024593 NC_000003.11:49394852:C:T NC_000003.12:49357419:C:T (self)
250623314, ss2251344215, ss3389831761, ss3709179306 NC_000003.12:49357419:C:T NC_000003.12:49357419:C:T (self)
ss10070307, ss11582997 NT_006014.14:509925:C:T NC_000003.12:49357419:C:T (self)
ss12568571, ss105435061, ss244304909 NT_022517.18:49334852:C:T NC_000003.12:49357419:C:T (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 rs6446261

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.post270+ab078da