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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.

rs2238289

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28208069 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.35693 (44819/125568, TOPMED)
G=0.2888 (9057/31358, GnomAD)
G=0.497 (2488/5008, 1000G) (+ 4 more)
G=0.145 (559/3854, ALSPAC)
G=0.135 (501/3708, TWINSUK)
G=0.08 (47/600, NorthernSweden)
A=0.22 (47/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
Publications
1 citation
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 15 NC_000015.10:g.28208069A>G
GRCh37.p13 chr 15 NC_000015.9:g.28453215A>G
HERC2 RefSeqGene NG_016355.1:g.119081T>C
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.341530A>G
Gene: HERC2, HECT and RLD domain containing E3 ubiquitin protein ligase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HERC2 transcript NM_004667.5:c. N/A Intron Variant
HERC2 transcript variant X3 XM_005268276.5:c. N/A Intron Variant
HERC2 transcript variant X1 XM_006720726.3:c. N/A Intron Variant
HERC2 transcript variant X5 XM_006720727.3:c. N/A Intron Variant
HERC2 transcript variant X2 XM_017022695.1:c. N/A Intron Variant
HERC2 transcript variant X4 XM_017022696.1:c. N/A Intron Variant
HERC2 transcript variant X8 XM_017022697.1:c. N/A Intron Variant
HERC2 transcript variant X9 XM_017022698.1:c. N/A Intron Variant
HERC2 transcript variant X7 XR_001751410.1:n. N/A Intron Variant
HERC2 transcript variant X6 XR_931930.2:n. N/A Intron 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 A=0.64307 G=0.35693
gnomAD - Genomes Global Study-wide 31358 A=0.7112 G=0.2888
gnomAD - Genomes European Sub 18896 A=0.9012 G=0.0988
gnomAD - Genomes African Sub 8680 A=0.364 G=0.636
gnomAD - Genomes East Asian Sub 1560 A=0.288 G=0.712
gnomAD - Genomes Other Sub 1086 A=0.828 G=0.172
gnomAD - Genomes American Sub 846 A=0.63 G=0.37
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.81 G=0.19
1000Genomes Global Study-wide 5008 A=0.503 G=0.497
1000Genomes African Sub 1322 A=0.298 G=0.702
1000Genomes East Asian Sub 1008 A=0.309 G=0.691
1000Genomes Europe Sub 1006 A=0.801 G=0.199
1000Genomes South Asian Sub 978 A=0.58 G=0.42
1000Genomes American Sub 694 A=0.64 G=0.36
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.855 G=0.145
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.865 G=0.135
Northern Sweden ACPOP Study-wide 600 A=0.92 G=0.08
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.22 G=0.78
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 A= G Note
GRCh38.p12 chr 15 NC_000015.10:g.28208069= NC_000015.10:g.28208069A>G
GRCh37.p13 chr 15 NC_000015.9:g.28453215= NC_000015.9:g.28453215A>G
HERC2 RefSeqGene NG_016355.1:g.119081= NG_016355.1:g.119081T>C
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.341530= NW_011332701.1:g.341530A>G
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#.

37 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3193194 Aug 15, 2001 (98)
2 BCM_SSAHASNP ss10777175 Jul 11, 2003 (117)
3 WI_SSAHASNP ss12321421 Jul 11, 2003 (117)
4 HGSV ss83737053 Dec 15, 2007 (130)
5 HGSV ss84230874 Dec 15, 2007 (130)
6 BGI ss103224370 Dec 01, 2009 (131)
7 ILLUMINA-UK ss118172203 Feb 14, 2009 (130)
8 GMI ss156361307 Dec 01, 2009 (131)
9 BUSHMAN ss200655447 Jul 04, 2010 (132)
10 1000GENOMES ss226813618 Jul 14, 2010 (132)
11 1000GENOMES ss236722830 Jul 15, 2010 (132)
12 1000GENOMES ss243120762 Jul 15, 2010 (132)
13 GMI ss282193184 May 04, 2012 (137)
14 SSMP ss660096236 Apr 25, 2013 (138)
15 EVA-GONL ss991625016 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1080003946 Aug 21, 2014 (142)
17 1000GENOMES ss1352825365 Aug 21, 2014 (142)
18 HAMMER_LAB ss1397692514 Sep 08, 2015 (146)
19 DDI ss1427576079 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1632672777 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1675666810 Apr 01, 2015 (144)
22 EVA_DECODE ss1695636794 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1935022444 Feb 12, 2016 (147)
24 GENOMED ss1968070876 Jul 19, 2016 (147)
25 JJLAB ss2028291313 Sep 14, 2016 (149)
26 USC_VALOUEV ss2156688383 Dec 20, 2016 (150)
27 TOPMED ss2370072851 Dec 20, 2016 (150)
28 GRF ss2701147505 Nov 08, 2017 (151)
29 GNOMAD ss2932999028 Nov 08, 2017 (151)
30 SWEGEN ss3013007454 Nov 08, 2017 (151)
31 TOPMED ss3223260907 Nov 08, 2017 (151)
32 CSHL ss3351042229 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3645373369 Oct 12, 2018 (152)
34 EVA_DECODE ss3697586162 Jul 13, 2019 (153)
35 ACPOP ss3740787781 Jul 13, 2019 (153)
36 EVA ss3752892461 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3818209556 Jul 13, 2019 (153)
38 1000Genomes NC_000015.9 - 28453215 Oct 12, 2018 (152)
39 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28453215 Oct 12, 2018 (152)
40 gnomAD - Genomes NC_000015.9 - 28453215 Jul 13, 2019 (153)
41 Northern Sweden NC_000015.9 - 28453215 Jul 13, 2019 (153)
42 TopMed NC_000015.10 - 28208069 Oct 12, 2018 (152)
43 UK 10K study - Twins NC_000015.9 - 28453215 Oct 12, 2018 (152)
44 A Vietnamese Genetic Variation Database NC_000015.9 - 28453215 Jul 13, 2019 (153)
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)
rs6497290 Aug 27, 2003 (117)
rs59484187 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss83737053, ss84230874, ss118172203, ss200655447, ss282193184, ss1397692514, ss1695636794 NC_000015.8:26126809:A:G NC_000015.10:28208068:A:G (self)
65872669, 36577032, 179706759, 14072646, 36577032, 8138326, ss226813618, ss236722830, ss243120762, ss660096236, ss991625016, ss1080003946, ss1352825365, ss1427576079, ss1632672777, ss1675666810, ss1935022444, ss1968070876, ss2028291313, ss2156688383, ss2370072851, ss2701147505, ss2932999028, ss3013007454, ss3351042229, ss3740787781, ss3752892461 NC_000015.9:28453214:A:G NC_000015.10:28208068:A:G (self)
125945171, ss3223260907, ss3645373369, ss3697586162, ss3818209556 NC_000015.10:28208068:A:G NC_000015.10:28208068:A:G (self)
ss10777175, ss12321421 NT_010280.15:812472:A:G NC_000015.10:28208068:A:G (self)
ss3193194, ss103224370, ss156361307 NT_026446.14:4888361:A:G NC_000015.10:28208068:A:G (self)
Help

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

1 citation for rs2238289
PMID Title Author Year Journal
20042077 Genetic determinants of hair and eye colours in the Scottish and Danish populations. Mengel-From J et al. 2009 BMC genetics

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.post104+4a6ee9c