Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

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.

rs58630086

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr17:6878094 (GRCh38.p7) 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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.06284 (7891/125568, TOPMED)
A=0.0532 (1646/30938, GnomAD)
A=0.079 (396/5008, 1000G) (+ 2 more)
A=0.045 (172/3854, ALSPAC)
A=0.039 (145/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ALOX12P2 : Intron 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.p7 chr 17 NC_000017.11:g.6878094G>A
GRCh38.p7 chr 17 NC_000017.11:g.6878094G>C
GRCh37.p13 chr 17 NC_000017.10:g.6781413G>A
GRCh37.p13 chr 17 NC_000017.10:g.6781413G>C
Gene: ALOX12P2, arachidonate 12-lipoxygenase pseudogene 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ALOX12P2 transcript variant 1 NR_002710.2:n. N/A Intron Variant
ALOX12P2 transcript variant 2 NR_120453.1:n. N/A Genic Upstream 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.

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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.93715 C=0.00001, A=0.06284
The Genome Aggregation Database Global Study-wide 30938 G=0.9468 A=0.0532
The Genome Aggregation Database European Sub 18492 G=0.9663 A=0.0337
The Genome Aggregation Database African Sub 8714 G=0.938 A=0.062
The Genome Aggregation Database East Asian Sub 1614 G=0.774 A=0.226
The Genome Aggregation Database Other Sub 978 G=0.97 A=0.03
The Genome Aggregation Database American Sub 838 G=0.90 A=0.10
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.98 A=0.02
1000Genomes Global Study-wide 5008 G=0.921 A=0.079
1000Genomes African Sub 1322 G=0.945 A=0.055
1000Genomes East Asian Sub 1008 G=0.799 A=0.201
1000Genomes Europe Sub 1006 G=0.969 A=0.031
1000Genomes South Asian Sub 978 G=0.98 A=0.02
1000Genomes American Sub 694 G=0.89 A=0.11
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.955 A=0.045
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.961 A=0.039
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 C Note
GRCh38.p7 chr 17 NC_000017.11:g.68...

NC_000017.11:g.6878094G=

NC_000017.11:g.68...

NC_000017.11:g.6878094G>A

NC_000017.11:g.68...

NC_000017.11:g.6878094G>C

GRCh37.p13 chr 17 NC_000017.10:g.67...

NC_000017.10:g.6781413G=

NC_000017.10:g.67...

NC_000017.10:g.6781413G>A

NC_000017.10:g.67...

NC_000017.10:g.6781413G>C

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#.

5 Frequency, 25 SubSNP submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81159695 Dec 15, 2007 (129)
2 GMI ss157805891 Dec 01, 2009 (131)
3 GMI ss282680310 May 04, 2012 (137)
4 1000GENOMES ss339536495 May 09, 2011 (134)
5 TISHKOFF ss565149069 Apr 25, 2013 (138)
6 SSMP ss660936446 Apr 25, 2013 (138)
7 EVA-GONL ss992893361 Aug 21, 2014 (142)
8 JMKIDD_LAB ss1080910776 Aug 21, 2014 (142)
9 1000GENOMES ss1357789979 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1635229151 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1678223184 Apr 01, 2015 (144)
12 EVA_DECODE ss1696933954 Apr 01, 2015 (144)
13 HAMMER_LAB ss1808689856 Sep 08, 2015 (146)
14 WEILL_CORNELL_DGM ss1936340025 Feb 12, 2016 (147)
15 JJLAB ss2028958217 Sep 14, 2016 (149)
16 USC_VALOUEV ss2157405066 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2215271101 Dec 20, 2016 (150)
18 TOPMED ss2380117655 Dec 20, 2016 (150)
19 SYSTEMSBIOZJU ss2628970969 Nov 08, 2017 (151)
20 GRF ss2701947690 Nov 08, 2017 (151)
21 GNOMAD ss2947366200 Nov 08, 2017 (151)
22 SWEGEN ss3015147241 Nov 08, 2017 (151)
23 TOPMED ss3256527543 Nov 08, 2017 (151)
24 TOPMED ss3256527544 Nov 08, 2017 (151)
25 CSHL ss3351639167 Nov 08, 2017 (151)
26 1000Genomes NC_000017.10 - 6781413 Jul 20, 2018 (151)
27 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 6781413 Jul 20, 2018 (151)
28 The Genome Aggregation Database NC_000017.10 - 6781413 Jul 20, 2018 (151)
29 Trans-Omics for Precision Medicine NC_000017.11 - 6878094 Jul 20, 2018 (151)
30 UK 10K study - Twins NC_000017.10 - 6781413 Jul 20, 2018 (151)
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
ss81159695, ss282680310, ss1696933954 NC_000017.9:6722136:G= NC_000017.11:6878093:G= (self)
70999671, 39378476, 81067728, 39378476, ss339536495, ss565149069, ss660936446, ss992893361, ss1080910776, ss1357789979, ss1635229151, ss1678223184, ss1808689856, ss1936340025, ss2028958217, ss2157405066, ss2380117655, ss2628970969, ss2701947690, ss2947366200, ss3015147241, ss3351639167 NC_000017.10:6781412:G= NC_000017.11:6878093:G= (self)
152277287, ss2215271101, ss3256527543, ss3256527544 NC_000017.11:6878093:G= NC_000017.11:6878093:G= (self)
ss157805891 NT_010718.16:6384786:G= NC_000017.11:6878093:G= (self)
ss81159695, ss282680310, ss1696933954 NC_000017.9:6722136:G>A NC_000017.11:6878093:G>A (self)
70999671, 39378476, 81067728, 39378476, ss339536495, ss565149069, ss660936446, ss992893361, ss1080910776, ss1357789979, ss1635229151, ss1678223184, ss1808689856, ss1936340025, ss2028958217, ss2157405066, ss2380117655, ss2628970969, ss2701947690, ss2947366200, ss3015147241, ss3351639167 NC_000017.10:6781412:G>A NC_000017.11:6878093:G>A (self)
152277287, ss2215271101, ss3256527543 NC_000017.11:6878093:G>A NC_000017.11:6878093:G>A (self)
ss157805891 NT_010718.16:6384786:G>A NC_000017.11:6878093:G>A (self)
152277287, ss3256527544 NC_000017.11:6878093:G>C NC_000017.11:6878093:G>C (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 rs58630086

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: 0.1.4.post833+d3ba21e