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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.

rs45495598

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr15:27957495 (GRCh38.p13) 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=0.045192 (11962/264690, TOPMED)
T=0.043218 (6060/140218, GnomAD)
T=0.04833 (913/18890, ALFA) (+ 15 more)
T=0.00310 (52/16760, 8.3KJPN)
T=0.0505 (253/5008, 1000G)
T=0.0348 (156/4480, Estonian)
T=0.0708 (273/3854, ALSPAC)
T=0.0574 (213/3708, TWINSUK)
T=0.0130 (38/2922, KOREAN)
T=0.058 (58/998, GoNL)
T=0.033 (20/600, NorthernSweden)
T=0.101 (54/534, MGP)
T=0.106 (23/216, Qatari)
T=0.009 (2/214, Vietnamese)
T=0.07 (3/40, GENOME_DK)
C=0.47 (18/38, SGDP_PRJ)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OCA2 : 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.p13 chr 15 NC_000015.10:g.27957495C>G
GRCh38.p13 chr 15 NC_000015.10:g.27957495C>T
GRCh37.p13 chr 15 NC_000015.9:g.28202641C>G
GRCh37.p13 chr 15 NC_000015.9:g.28202641C>T
OCA2 RefSeqGene NG_009846.1:g.146818G>C
OCA2 RefSeqGene NG_009846.1:g.146818G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.91782C>G
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.91782C>T
GRCh38.p13 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.91782C>G
GRCh38.p13 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.91782C>T
Gene: OCA2, OCA2 melanosomal transmembrane protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OCA2 transcript variant 1 NM_000275.3:c.1784+93G>C N/A Intron Variant
OCA2 transcript variant 2 NM_001300984.2:c.1712+93G…

NM_001300984.2:c.1712+93G>C

N/A Intron Variant
OCA2 transcript variant X2 XM_011521640.2:c.1784+93G…

XM_011521640.2:c.1784+93G>C

N/A Intron Variant
OCA2 transcript variant X1 XM_017022255.1:c.1808+93G…

XM_017022255.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X3 XM_017022256.1:c.1808+93G…

XM_017022256.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X4 XM_017022257.1:c.1736+93G…

XM_017022257.1:c.1736+93G>C

N/A Intron Variant
OCA2 transcript variant X5 XM_017022258.1:c.1808+93G…

XM_017022258.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X6 XM_017022259.1:c.1736+93G…

XM_017022259.1:c.1736+93G>C

N/A Intron Variant
OCA2 transcript variant X7 XM_017022260.1:c.1670+93G…

XM_017022260.1:c.1670+93G>C

N/A Intron Variant
OCA2 transcript variant X8 XM_017022261.1:c.1613+93G…

XM_017022261.1:c.1613+93G>C

N/A Intron Variant
OCA2 transcript variant X9 XM_017022262.1:c.1808+93G…

XM_017022262.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X10 XM_017022263.1:c.1808+93G…

XM_017022263.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X11 XM_017022264.1:c.1808+93G…

XM_017022264.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X12 XM_017022265.1:c.1808+93G…

XM_017022265.1:c.1808+93G>C

N/A Intron Variant
OCA2 transcript variant X13 XR_001751294.1:n. N/A Genic Downstream 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.95167 T=0.04833
European Sub 14286 C=0.94596 T=0.05404
African Sub 2946 C=0.9854 T=0.0146
African Others Sub 114 C=1.000 T=0.000
African American Sub 2832 C=0.9848 T=0.0152
Asian Sub 112 C=0.991 T=0.009
East Asian Sub 86 C=0.99 T=0.01
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.925 T=0.075
Latin American 2 Sub 610 C=0.957 T=0.043
South Asian Sub 98 C=0.77 T=0.23
Other Sub 692 C=0.947 T=0.053


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 C=0.954808 T=0.045192
gnomAD - Genomes Global Study-wide 140218 C=0.956782 T=0.043218
gnomAD - Genomes European Sub 75926 C=0.94558 T=0.05442
gnomAD - Genomes African Sub 42036 C=0.98925 T=0.01075
gnomAD - Genomes American Sub 13658 C=0.93550 T=0.06450
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.8602 T=0.1398
gnomAD - Genomes East Asian Sub 3128 C=0.9917 T=0.0083
gnomAD - Genomes Other Sub 2152 C=0.9512 T=0.0488
8.3KJPN JAPANESE Study-wide 16760 C=0.99690 T=0.00310
1000Genomes Global Study-wide 5008 C=0.9495 T=0.0505
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=0.9950 T=0.0050
1000Genomes Europe Sub 1006 C=0.9235 T=0.0765
1000Genomes South Asian Sub 978 C=0.865 T=0.135
1000Genomes American Sub 694 C=0.947 T=0.053
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9652 T=0.0348
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9292 T=0.0708
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9426 T=0.0574
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9870 T=0.0130
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.942 T=0.058
Northern Sweden ACPOP Study-wide 600 C=0.967 T=0.033
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.899 T=0.101
Qatari Global Study-wide 216 C=0.894 T=0.106
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.991 T=0.009
The Danish reference pan genome Danish Study-wide 40 C=0.93 T=0.07
SGDP_PRJ Global Study-wide 38 C=0.47 T=0.53
Siberian Global Study-wide 6 C=0.5 T=0.5
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
GRCh38.p13 chr 15 NC_000015.10:g.27957495= NC_000015.10:g.27957495C>G NC_000015.10:g.27957495C>T
GRCh37.p13 chr 15 NC_000015.9:g.28202641= NC_000015.9:g.28202641C>G NC_000015.9:g.28202641C>T
OCA2 RefSeqGene NG_009846.1:g.146818= NG_009846.1:g.146818G>C NG_009846.1:g.146818G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.91782= NW_011332701.1:g.91782C>G NW_011332701.1:g.91782C>T
GRCh38.p13 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.91782= NT_187660.1:g.91782C>G NT_187660.1:g.91782C>T
OCA2 transcript variant 1 NM_000275.2:c.1784+93= NM_000275.2:c.1784+93G>C NM_000275.2:c.1784+93G>A
OCA2 transcript variant 1 NM_000275.3:c.1784+93= NM_000275.3:c.1784+93G>C NM_000275.3:c.1784+93G>A
OCA2 transcript variant 2 NM_001300984.2:c.1712+93= NM_001300984.2:c.1712+93G>C NM_001300984.2:c.1712+93G>A
OCA2 transcript variant X1 XM_005268259.1:c.1712+93= XM_005268259.1:c.1712+93G>C XM_005268259.1:c.1712+93G>A
OCA2 transcript variant X2 XM_011521640.2:c.1784+93= XM_011521640.2:c.1784+93G>C XM_011521640.2:c.1784+93G>A
OCA2 transcript variant X1 XM_017022255.1:c.1808+93= XM_017022255.1:c.1808+93G>C XM_017022255.1:c.1808+93G>A
OCA2 transcript variant X3 XM_017022256.1:c.1808+93= XM_017022256.1:c.1808+93G>C XM_017022256.1:c.1808+93G>A
OCA2 transcript variant X4 XM_017022257.1:c.1736+93= XM_017022257.1:c.1736+93G>C XM_017022257.1:c.1736+93G>A
OCA2 transcript variant X5 XM_017022258.1:c.1808+93= XM_017022258.1:c.1808+93G>C XM_017022258.1:c.1808+93G>A
OCA2 transcript variant X6 XM_017022259.1:c.1736+93= XM_017022259.1:c.1736+93G>C XM_017022259.1:c.1736+93G>A
OCA2 transcript variant X7 XM_017022260.1:c.1670+93= XM_017022260.1:c.1670+93G>C XM_017022260.1:c.1670+93G>A
OCA2 transcript variant X8 XM_017022261.1:c.1613+93= XM_017022261.1:c.1613+93G>C XM_017022261.1:c.1613+93G>A
OCA2 transcript variant X9 XM_017022262.1:c.1808+93= XM_017022262.1:c.1808+93G>C XM_017022262.1:c.1808+93G>A
OCA2 transcript variant X10 XM_017022263.1:c.1808+93= XM_017022263.1:c.1808+93G>C XM_017022263.1:c.1808+93G>A
OCA2 transcript variant X11 XM_017022264.1:c.1808+93= XM_017022264.1:c.1808+93G>C XM_017022264.1:c.1808+93G>A
OCA2 transcript variant X12 XM_017022265.1:c.1808+93= XM_017022265.1:c.1808+93G>C XM_017022265.1:c.1808+93G>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#.

35 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss69374775 May 17, 2007 (127)
2 1000GENOMES ss236722393 Jul 15, 2010 (132)
3 SSMP ss660095211 Apr 25, 2013 (138)
4 EVA-GONL ss991623664 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1080002747 Aug 21, 2014 (142)
6 1000GENOMES ss1352818274 Aug 21, 2014 (142)
7 DDI ss1427575691 Apr 01, 2015 (144)
8 EVA_GENOME_DK ss1577522594 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1632669714 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1675663747 Apr 01, 2015 (144)
11 EVA_DECODE ss1695635219 Apr 01, 2015 (144)
12 EVA_MGP ss1711390073 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1935020740 Feb 12, 2016 (147)
14 JJLAB ss2028290685 Sep 14, 2016 (149)
15 USC_VALOUEV ss2156687661 Dec 20, 2016 (150)
16 HUMAN_LONGEVITY ss2205522321 Dec 20, 2016 (150)
17 TOPMED ss2370057669 Dec 20, 2016 (150)
18 SYSTEMSBIOZJU ss2628638460 Nov 08, 2017 (151)
19 GRF ss2701146682 Nov 08, 2017 (151)
20 GNOMAD ss2932978507 Nov 08, 2017 (151)
21 SWEGEN ss3013004990 Nov 08, 2017 (151)
22 TOPMED ss3223214756 Nov 08, 2017 (151)
23 CSHL ss3351041687 Nov 08, 2017 (151)
24 OMUKHERJEE_ADBS ss3646469594 Oct 12, 2018 (152)
25 EGCUT_WGS ss3680176505 Jul 13, 2019 (153)
26 EVA_DECODE ss3697583189 Jul 13, 2019 (153)
27 ACPOP ss3740786691 Jul 13, 2019 (153)
28 EVA ss3752890508 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3818207759 Jul 13, 2019 (153)
30 EVA ss3834156328 Apr 27, 2020 (154)
31 SGDP_PRJ ss3882550523 Apr 27, 2020 (154)
32 KRGDB ss3931674414 Apr 27, 2020 (154)
33 VINODS ss4031998967 Apr 26, 2021 (155)
34 TOPMED ss4985694677 Apr 26, 2021 (155)
35 TOMMO_GENOMICS ss5215401822 Apr 26, 2021 (155)
36 1000Genomes NC_000015.9 - 28202641 Oct 12, 2018 (152)
37 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28202641 Oct 12, 2018 (152)
38 Genetic variation in the Estonian population NC_000015.9 - 28202641 Oct 12, 2018 (152)
39 The Danish reference pan genome NC_000015.9 - 28202641 Apr 27, 2020 (154)
40 gnomAD - Genomes NC_000015.10 - 27957495 Apr 26, 2021 (155)
41 Genome of the Netherlands Release 5 NC_000015.9 - 28202641 Apr 27, 2020 (154)
42 KOREAN population from KRGDB NC_000015.9 - 28202641 Apr 27, 2020 (154)
43 Medical Genome Project healthy controls from Spanish population NC_000015.9 - 28202641 Apr 27, 2020 (154)
44 Northern Sweden NC_000015.9 - 28202641 Jul 13, 2019 (153)
45 Qatari NC_000015.9 - 28202641 Apr 27, 2020 (154)
46 SGDP_PRJ NC_000015.9 - 28202641 Apr 27, 2020 (154)
47 Siberian NC_000015.9 - 28202641 Apr 27, 2020 (154)
48 8.3KJPN NC_000015.9 - 28202641 Apr 26, 2021 (155)
49 TopMed NC_000015.10 - 27957495 Apr 26, 2021 (155)
50 UK 10K study - Twins NC_000015.9 - 28202641 Oct 12, 2018 (152)
51 A Vietnamese Genetic Variation Database NC_000015.9 - 28202641 Jul 13, 2019 (153)
52 ALFA NC_000015.10 - 27957495 Apr 26, 2021 (155)
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
ss2205522321 NC_000015.10:27957494:C:G NC_000015.10:27957494:C:G (self)
ss1695635219 NC_000015.8:25876235:C:T NC_000015.10:27957494:C:T (self)
65865301, 36573639, 25914753, 3792394, 16337605, 38851808, 505833, 14071556, 17062670, 34567503, 9204015, 73371129, 36573639, 8137581, ss236722393, ss660095211, ss991623664, ss1080002747, ss1352818274, ss1427575691, ss1577522594, ss1632669714, ss1675663747, ss1711390073, ss1935020740, ss2028290685, ss2156687661, ss2370057669, ss2628638460, ss2701146682, ss2932978507, ss3013004990, ss3351041687, ss3646469594, ss3680176505, ss3740786691, ss3752890508, ss3834156328, ss3882550523, ss3931674414, ss5215401822 NC_000015.9:28202640:C:T NC_000015.10:27957494:C:T (self)
464255681, 125906972, 201240337, 4687568499, ss2205522321, ss3223214756, ss3697583189, ss3818207759, ss4985694677 NC_000015.10:27957494:C:T NC_000015.10:27957494:C:T (self)
ss69374775 NT_026446.14:4637787:C:T NC_000015.10:27957494:C:T (self)
ss4031998967 NT_187660.1:91781:C:T NC_000015.10:27957494:C:T
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 rs45495598
PMID Title Author Year Journal
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
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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.post596+ae089ad