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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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr15:28023862 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.48172 (60489/125568, TOPMED)
C=0.4243 (13249/31224, GnomAD)
A=0.377 (1888/5008, 1000G) (+ 3 more)
C=0.203 (782/3854, ALSPAC)
C=0.208 (773/3708, TWINSUK)
C=0.17 (105/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OCA2 : Intron Variant
0 citations
Genomic View
See rs on genome

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.28023862A>C
GRCh37.p13 chr 15 NC_000015.9:g.28269008A>C
OCA2 RefSeqGene NG_009846.1:g.80451T>G
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.158161A>C
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.158161A>C
Gene: OCA2, OCA2 melanosomal transmembrane protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OCA2 transcript variant 1 NM_000275.3:c. N/A Intron Variant
OCA2 transcript variant 2 NM_001300984.2:c. N/A Intron Variant
OCA2 transcript variant X2 XM_011521640.2:c. N/A Intron Variant
OCA2 transcript variant X1 XM_017022255.1:c. N/A Intron Variant
OCA2 transcript variant X3 XM_017022256.1:c. N/A Intron Variant
OCA2 transcript variant X4 XM_017022257.1:c. N/A Intron Variant
OCA2 transcript variant X5 XM_017022258.1:c. N/A Intron Variant
OCA2 transcript variant X6 XM_017022259.1:c. N/A Intron Variant
OCA2 transcript variant X7 XM_017022260.1:c. N/A Intron Variant
OCA2 transcript variant X8 XM_017022261.1:c. N/A Intron Variant
OCA2 transcript variant X9 XM_017022262.1:c. N/A Intron Variant
OCA2 transcript variant X10 XM_017022263.1:c. N/A Intron Variant
OCA2 transcript variant X11 XM_017022264.1:c. N/A Intron Variant
OCA2 transcript variant X12 XM_017022265.1:c. N/A Intron Variant
OCA2 transcript variant X13 XR_001751294.1:n. 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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.51828 C=0.48172
gnomAD - Genomes Global Study-wide 31224 A=0.5757 C=0.4243
gnomAD - Genomes European Sub 18830 A=0.8005 C=0.1995
gnomAD - Genomes African Sub 8658 A=0.138 C=0.862
gnomAD - Genomes East Asian Sub 1526 A=0.122 C=0.878
gnomAD - Genomes Other Sub 1080 A=0.719 C=0.281
gnomAD - Genomes American Sub 842 A=0.65 C=0.35
gnomAD - Genomes Ashkenazi Jewish Sub 288 A=0.68 C=0.32
1000Genomes Global Study-wide 5008 A=0.377 C=0.623
1000Genomes African Sub 1322 A=0.042 C=0.958
1000Genomes East Asian Sub 1008 A=0.107 C=0.893
1000Genomes Europe Sub 1006 A=0.760 C=0.240
1000Genomes South Asian Sub 978 A=0.55 C=0.45
1000Genomes American Sub 694 A=0.61 C=0.39
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.797 C=0.203
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.792 C=0.208
Northern Sweden ACPOP Study-wide 600 A=0.82 C=0.17

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 Note
GRCh38.p12 chr 15 NC_000015.10:g.28023862= NC_000015.10:g.28023862A>C
GRCh37.p13 chr 15 NC_000015.9:g.28269008= NC_000015.9:g.28269008A>C
OCA2 RefSeqGene NG_009846.1:g.80451= NG_009846.1:g.80451T>G
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.158161= NW_011332701.1:g.158161A>C
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.158161= NT_187660.1:g.158161A>C

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#.

49 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4980980 Aug 28, 2002 (107)
2 SC_JCM ss5708096 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10794348 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss20012035 Feb 27, 2004 (120)
5 ABI ss40531436 Mar 15, 2006 (126)
6 PERLEGEN ss69171474 May 17, 2007 (127)
7 HGSV ss80724796 Dec 16, 2007 (130)
8 HGSV ss83599986 Dec 16, 2007 (130)
9 HGSV ss83899866 Dec 16, 2007 (130)
10 HGSV ss84438279 Dec 16, 2007 (130)
11 BGI ss106418871 Feb 06, 2009 (130)
12 1000GENOMES ss108695937 Jan 23, 2009 (130)
13 1000GENOMES ss113953254 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118171793 Feb 14, 2009 (130)
15 GMI ss156359984 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168984481 Jul 04, 2010 (132)
17 BUSHMAN ss200653816 Jul 04, 2010 (132)
18 1000GENOMES ss226812993 Jul 14, 2010 (132)
19 1000GENOMES ss236722517 Jul 15, 2010 (132)
20 1000GENOMES ss243120527 Jul 15, 2010 (132)
21 GMI ss282192799 May 04, 2012 (137)
22 GMI ss286924615 Apr 25, 2013 (138)
23 PJP ss291808255 May 09, 2011 (134)
24 TISHKOFF ss564383410 Apr 25, 2013 (138)
25 SSMP ss660095500 Apr 25, 2013 (138)
26 EVA-GONL ss991624060 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1080003088 Aug 21, 2014 (142)
28 1000GENOMES ss1352820160 Aug 21, 2014 (142)
29 DDI ss1427575833 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1577522805 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1632670617 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1675664650 Apr 01, 2015 (144)
33 HAMMER_LAB ss1808131188 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1935021096 Feb 12, 2016 (147)
35 JJLAB ss2028290885 Sep 14, 2016 (149)
36 USC_VALOUEV ss2156687874 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2205526240 Dec 20, 2016 (150)
38 TOPMED ss2370061661 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2628638604 Nov 08, 2017 (151)
40 GRF ss2701146901 Nov 08, 2017 (151)
41 GNOMAD ss2932983666 Nov 08, 2017 (151)
42 SWEGEN ss3013005629 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3027969691 Nov 08, 2017 (151)
44 TOPMED ss3223226541 Nov 08, 2017 (151)
45 CSHL ss3351041861 Nov 08, 2017 (151)
46 EVA_DECODE ss3697583998 Jul 13, 2019 (153)
47 ACPOP ss3740787001 Jul 13, 2019 (153)
48 EVA ss3752891013 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3818208232 Jul 13, 2019 (153)
50 1000Genomes NC_000015.9 - 28269008 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28269008 Oct 12, 2018 (152)
52 gnomAD - Genomes NC_000015.9 - 28269008 Jul 13, 2019 (153)
53 Northern Sweden NC_000015.9 - 28269008 Jul 13, 2019 (153)
54 TopMed NC_000015.10 - 28023862 Oct 12, 2018 (152)
55 UK 10K study - Twins NC_000015.9 - 28269008 Oct 12, 2018 (152)

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)
rs61060677 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss80724796, ss83599986, ss83899866, ss84438279, ss108695937, ss113953254, ss118171793, ss168984481, ss200653816, ss282192799, ss286924615, ss291808255 NC_000015.8:25942602:A:C NC_000015.10:28023861:A:C (self)
65867243, 36574626, 179691863, 14071866, 36574626, ss226812993, ss236722517, ss243120527, ss564383410, ss660095500, ss991624060, ss1080003088, ss1352820160, ss1427575833, ss1577522805, ss1632670617, ss1675664650, ss1808131188, ss1935021096, ss2028290885, ss2156687874, ss2370061661, ss2628638604, ss2701146901, ss2932983666, ss3013005629, ss3351041861, ss3740787001, ss3752891013 NC_000015.9:28269007:A:C NC_000015.10:28023861:A:C (self)
125917005, ss2205526240, ss3027969691, ss3223226541, ss3697583998, ss3818208232 NC_000015.10:28023861:A:C NC_000015.10:28023861:A:C (self)
ss10794348 NT_010280.15:634498:A:C NC_000015.10:28023861:A:C (self)
ss20012035 NT_010280.16:634498:A:C NC_000015.10:28023861:A:C (self)
ss4980980, ss5708096, ss40531436, ss69171474, ss106418871, ss156359984 NT_026446.14:4704154:A:C NC_000015.10:28023861:A:C (self)

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

No publications for rs3794606

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