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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.

rs885479

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:89919746 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.15154 (37008/244212, GnomAD_exome)
A=0.10043 (12611/125568, TOPMED)
A=0.13583 (16166/119016, ExAC) (+ 8 more)
A=0.1005 (3148/31334, GnomAD)
A=0.0371 (481/12976, GO-ESP)
A=0.191 (958/5008, 1000G)
A=0.079 (355/4480, Estonian)
A=0.042 (163/3854, ALSPAC)
A=0.038 (140/3708, TWINSUK)
G=0.42 (257/612, Vietnamese)
A=0.09 (53/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MC1R : Missense Variant
Publications
23 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 16 NC_000016.10:g.89919746G>A
GRCh37.p13 chr 16 NC_000016.9:g.89986154G>A
TUBB3 RefSeqGene NG_027810.1:g.2738G>A
MC1R RefSeqGene NG_012026.1:g.6868G>A
Gene: MC1R, melanocortin 1 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MC1R transcript NM_002386.3:c.488G>A R [CGA] > Q [CAA] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Arg163Gln R (Arg) > Q (Gln) Missense Variant
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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.

Allele: A (allele ID: 256010 )
ClinVar Accession Disease Names Clinical Significance
RCV000248045.1 not specified Benign
RCV000263355.1 Malignant Melanoma Susceptibility Benign
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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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 244212 G=0.84846 A=0.15154
gnomAD - Exomes European Sub 129760 G=0.92711 A=0.07289
gnomAD - Exomes Asian Sub 48486 G=0.7400 A=0.2600
gnomAD - Exomes American Sub 34476 G=0.6035 A=0.3965
gnomAD - Exomes African Sub 15472 G=0.9834 A=0.0166
gnomAD - Exomes Ashkenazi Jewish Sub 10000 G=0.9656 A=0.0344
gnomAD - Exomes Other Sub 6018 G=0.889 A=0.111
TopMed Global Study-wide 125568 G=0.89957 A=0.10043
ExAC Global Study-wide 119016 G=0.86417 A=0.13583
ExAC Europe Sub 71928 G=0.9308 A=0.0692
ExAC Asian Sub 25000 G=0.7553 A=0.2447
ExAC American Sub 11512 G=0.5844 A=0.4156
ExAC African Sub 9692 G=0.982 A=0.018
ExAC Other Sub 884 G=0.87 A=0.13
gnomAD - Genomes Global Study-wide 31334 G=0.8995 A=0.1005
gnomAD - Genomes European Sub 18872 G=0.9159 A=0.0841
gnomAD - Genomes African Sub 8694 G=0.981 A=0.019
gnomAD - Genomes East Asian Sub 1544 G=0.376 A=0.624
gnomAD - Genomes Other Sub 1088 G=0.868 A=0.132
gnomAD - Genomes American Sub 848 G=0.67 A=0.33
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.96 A=0.04
GO Exome Sequencing Project Global Study-wide 12976 G=0.9629 A=0.0371
GO Exome Sequencing Project European American Sub 8588 G=0.952 A=0.048
GO Exome Sequencing Project African American Sub 4388 G=0.985 A=0.015
1000Genomes Global Study-wide 5008 G=0.809 A=0.191
1000Genomes African Sub 1322 G=0.993 A=0.007
1000Genomes East Asian Sub 1008 G=0.384 A=0.616
1000Genomes Europe Sub 1006 G=0.930 A=0.070
1000Genomes South Asian Sub 978 G=0.96 A=0.04
1000Genomes American Sub 694 G=0.68 A=0.32
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.921 A=0.079
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.958 A=0.042
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.962 A=0.038
A Vietnamese Genetic Variation Database Global Study-wide 612 G=0.42 A=0.58
Northern Sweden ACPOP Study-wide 600 G=0.91 A=0.09
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 Note
GRCh38.p12 chr 16 NC_000016.10:g.89919746= NC_000016.10:g.89919746G>A
GRCh37.p13 chr 16 NC_000016.9:g.89986154= NC_000016.9:g.89986154G>A
TUBB3 RefSeqGene NG_027810.1:g.2738= NG_027810.1:g.2738G>A
MC1R RefSeqGene NG_012026.1:g.6868= NG_012026.1:g.6868G>A
MC1R transcript NM_002386.3:c.488= NM_002386.3:c.488G>A
melanocyte-stimulating hormone receptor NP_002377.4:p.Arg163= NP_002377.4:p.Arg163Gln
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#.

104 SubSNP, 11 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1313046 Oct 05, 2000 (86)
2 LEE ss1510341 Oct 05, 2000 (92)
3 PGA-UW-FHCRC ss4472738 Jul 03, 2002 (106)
4 SNP500CANCER ss48295633 Mar 13, 2006 (126)
5 APPLERA_GI ss48410318 Mar 13, 2006 (126)
6 RIKENSNPRC ss49848777 Mar 13, 2006 (126)
7 ILLUMINA ss65732100 Oct 16, 2006 (127)
8 ILLUMINA ss66567408 Nov 30, 2006 (127)
9 ILLUMINA ss67887538 Nov 30, 2006 (127)
10 ILLUMINA ss68025640 Nov 30, 2006 (127)
11 ILLUMINA ss70978413 May 23, 2008 (130)
12 ILLUMINA ss71590279 May 17, 2007 (127)
13 ILLUMINA ss75746584 Dec 07, 2007 (129)
14 ILLUMINA ss79286716 Dec 14, 2007 (130)
15 KRIBB_YJKIM ss83594321 Dec 14, 2007 (130)
16 BGI ss103323810 Dec 01, 2009 (131)
17 ILLUMINA ss122934171 Dec 01, 2009 (131)
18 ILLUMINA ss154477609 Dec 01, 2009 (131)
19 ILLUMINA ss159652044 Dec 01, 2009 (131)
20 ILLUMINA ss160962733 Dec 01, 2009 (131)
21 ILLUMINA ss172420880 Jul 04, 2010 (132)
22 ILLUMINA ss174766509 Jul 04, 2010 (132)
23 1000GENOMES ss237150931 Jul 15, 2010 (132)
24 1000GENOMES ss243467203 Jul 15, 2010 (132)
25 ILLUMINA ss244313521 Jul 04, 2010 (132)
26 GMI ss282656952 May 04, 2012 (137)
27 ILLUMINA ss481825100 May 04, 2012 (137)
28 ILLUMINA ss481857614 May 04, 2012 (137)
29 ILLUMINA ss482816965 Sep 08, 2015 (146)
30 ILLUMINA ss485707079 May 04, 2012 (137)
31 EXOME_CHIP ss491513806 May 04, 2012 (137)
32 CLINSEQ_SNP ss491725594 May 04, 2012 (137)
33 ILLUMINA ss537570726 Sep 08, 2015 (146)
34 SSMP ss660892028 Apr 25, 2013 (138)
35 NHLBI-ESP ss713334843 Apr 25, 2013 (138)
36 ILLUMINA ss778631097 Sep 08, 2015 (146)
37 ILLUMINA ss780722559 Sep 08, 2015 (146)
38 ILLUMINA ss783299147 Sep 08, 2015 (146)
39 ILLUMINA ss783398387 Sep 08, 2015 (146)
40 ILLUMINA ss784251503 Sep 08, 2015 (146)
41 ILLUMINA ss825617234 Apr 01, 2015 (144)
42 ILLUMINA ss832560485 Sep 08, 2015 (146)
43 ILLUMINA ss833162853 Jul 13, 2019 (153)
44 ILLUMINA ss834088707 Sep 08, 2015 (146)
45 EVA-GONL ss992830733 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1067565422 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1080869836 Aug 21, 2014 (142)
48 1000GENOMES ss1357561459 Aug 21, 2014 (142)
49 EVA_GENOME_DK ss1578051495 Apr 01, 2015 (144)
50 EVA_FINRISK ss1584102415 Apr 01, 2015 (144)
51 EVA_UK10K_ALSPAC ss1635117244 Apr 01, 2015 (144)
52 EVA_UK10K_TWINSUK ss1678111277 Apr 01, 2015 (144)
53 EVA_EXAC ss1692487512 Apr 01, 2015 (144)
54 EVA_DECODE ss1696872311 Apr 01, 2015 (144)
55 EVA_MGP ss1711441358 Apr 01, 2015 (144)
56 EVA_SVP ss1713563809 Apr 01, 2015 (144)
57 ILLUMINA ss1752213144 Sep 08, 2015 (146)
58 ILLUMINA ss1752213145 Sep 08, 2015 (146)
59 ILLUMINA ss1917911994 Feb 12, 2016 (147)
60 WEILL_CORNELL_DGM ss1936272974 Feb 12, 2016 (147)
61 ILLUMINA ss1946424255 Feb 12, 2016 (147)
62 GENOMED ss1968333625 Jul 19, 2016 (147)
63 JJLAB ss2028926299 Sep 14, 2016 (149)
64 USC_VALOUEV ss2157367880 Dec 20, 2016 (150)
65 HUMAN_LONGEVITY ss2214824200 Dec 20, 2016 (150)
66 TOPMED ss2379650270 Dec 20, 2016 (150)
67 ILLUMINA ss2633363344 Nov 08, 2017 (151)
68 ILLUMINA ss2635067381 Nov 08, 2017 (151)
69 GRF ss2701904643 Nov 08, 2017 (151)
70 GNOMAD ss2742271378 Nov 08, 2017 (151)
71 GNOMAD ss2749635813 Nov 08, 2017 (151)
72 GNOMAD ss2946702246 Nov 08, 2017 (151)
73 AFFY ss2985080458 Nov 08, 2017 (151)
74 SWEGEN ss3015041399 Nov 08, 2017 (151)
75 TOPMED ss3255026662 Nov 08, 2017 (151)
76 ILLUMINA ss3625702177 Oct 12, 2018 (152)
77 ILLUMINA ss3631346739 Oct 12, 2018 (152)
78 ILLUMINA ss3633838993 Oct 12, 2018 (152)
79 ILLUMINA ss3634658694 Oct 12, 2018 (152)
80 ILLUMINA ss3635527018 Oct 12, 2018 (152)
81 ILLUMINA ss3636350097 Oct 12, 2018 (152)
82 ILLUMINA ss3637278513 Oct 12, 2018 (152)
83 ILLUMINA ss3638143985 Oct 12, 2018 (152)
84 ILLUMINA ss3639083123 Oct 12, 2018 (152)
85 ILLUMINA ss3639547987 Oct 12, 2018 (152)
86 ILLUMINA ss3640366014 Oct 12, 2018 (152)
87 ILLUMINA ss3641075780 Oct 12, 2018 (152)
88 ILLUMINA ss3641371282 Oct 12, 2018 (152)
89 ILLUMINA ss3643123679 Oct 12, 2018 (152)
90 BIOINF_KMB_FNS_UNIBA ss3645435733 Oct 12, 2018 (152)
91 OMUKHERJEE_ADBS ss3646500356 Oct 12, 2018 (152)
92 ILLUMINA ss3653852555 Oct 12, 2018 (152)
93 EGCUT_WGS ss3682019201 Jul 13, 2019 (153)
94 EVA_DECODE ss3699905751 Jul 13, 2019 (153)
95 ACPOP ss3741791961 Jul 13, 2019 (153)
96 ILLUMINA ss3744436943 Jul 13, 2019 (153)
97 ILLUMINA ss3744959057 Jul 13, 2019 (153)
98 EVA ss3754343128 Jul 13, 2019 (153)
99 ILLUMINA ss3772457161 Jul 13, 2019 (153)
100 ILLUMINA ss3772457162 Jul 13, 2019 (153)
101 PACBIO ss3788124135 Jul 13, 2019 (153)
102 PACBIO ss3793095030 Jul 13, 2019 (153)
103 PACBIO ss3797980432 Jul 13, 2019 (153)
104 KHV_HUMAN_GENOMES ss3819613408 Jul 13, 2019 (153)
105 1000Genomes NC_000016.9 - 89986154 Oct 12, 2018 (152)
106 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 89986154 Oct 12, 2018 (152)
107 Genetic variation in the Estonian population NC_000016.9 - 89986154 Oct 12, 2018 (152)
108 ExAC NC_000016.9 - 89986154 Oct 12, 2018 (152)
109 gnomAD - Genomes NC_000016.9 - 89986154 Jul 13, 2019 (153)
110 gnomAD - Exomes NC_000016.9 - 89986154 Jul 13, 2019 (153)
111 GO Exome Sequencing Project NC_000016.9 - 89986154 Oct 12, 2018 (152)
112 Northern Sweden NC_000016.9 - 89986154 Jul 13, 2019 (153)
113 TopMed NC_000016.10 - 89919746 Oct 12, 2018 (152)
114 UK 10K study - Twins NC_000016.9 - 89986154 Oct 12, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000016.9 - 89986154 Jul 13, 2019 (153)
116 ClinVar RCV000248045.1 Oct 12, 2018 (152)
117 ClinVar RCV000263355.1 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)
rs1042809 Jan 18, 2001 (92)
rs56959934 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss282656952, ss481825100, ss491725594, ss825617234, ss1696872311, ss1713563809, ss2635067381, ss3639083123, ss3639547987, ss3643123679 NC_000016.8:88513654:G:A NC_000016.10:89919745:G:A (self)
70762822, 39253513, 27757449, 2907968, 193093869, 11564266, 1511038, 15076826, 39253513, 8697222, ss237150931, ss243467203, ss481857614, ss482816965, ss485707079, ss491513806, ss537570726, ss660892028, ss713334843, ss778631097, ss780722559, ss783299147, ss783398387, ss784251503, ss832560485, ss833162853, ss834088707, ss992830733, ss1067565422, ss1080869836, ss1357561459, ss1578051495, ss1584102415, ss1635117244, ss1678111277, ss1692487512, ss1711441358, ss1752213144, ss1752213145, ss1917911994, ss1936272974, ss1946424255, ss1968333625, ss2028926299, ss2157367880, ss2379650270, ss2633363344, ss2701904643, ss2742271378, ss2749635813, ss2946702246, ss2985080458, ss3015041399, ss3625702177, ss3631346739, ss3633838993, ss3634658694, ss3635527018, ss3636350097, ss3637278513, ss3638143985, ss3640366014, ss3641075780, ss3641371282, ss3646500356, ss3653852555, ss3682019201, ss3741791961, ss3744436943, ss3744959057, ss3754343128, ss3772457161, ss3772457162, ss3788124135, ss3793095030, ss3797980432 NC_000016.9:89986153:G:A NC_000016.10:89919745:G:A (self)
RCV000248045.1, RCV000263355.1, 151103903, ss2214824200, ss3255026662, ss3645435733, ss3699905751, ss3819613408 NC_000016.10:89919745:G:A NC_000016.10:89919745:G:A (self)
ss1313046, ss1510341, ss4472738, ss48295633, ss48410318, ss49848777, ss65732100, ss66567408, ss67887538, ss68025640, ss70978413, ss71590279, ss75746584, ss79286716, ss83594321, ss103323810, ss122934171, ss154477609, ss159652044, ss160962733, ss172420880, ss174766509, ss244313521 NT_010542.15:1546770:G:A NC_000016.10:89919745:G:A (self)
Help

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

23 citations for rs885479
PMID Title Author Year Journal
11487574 The melanocortin-1-receptor gene is the major freckle gene. Bastiaens M et al. 2001 Human molecular genetics
11511307 Melanocortin 1 receptor (MC1R) gene variants are associated with an increased risk for cutaneous melanoma which is largely independent of skin type and hair color. Kennedy C et al. 2001 The Journal of investigative dermatology
17434924 MC1R: three novel variants identified in a malignant melanoma association study in the Spanish population. Fernandez L et al. 2007 Carcinogenesis
17616515 Receptor function, dominant negative activity and phenotype correlations for MC1R variant alleles. Beaumont KA et al. 2007 Human molecular genetics
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
18366057 MC1R variants, melanoma and red hair color phenotype: a meta-analysis. Raimondi S et al. 2008 International journal of cancer
19503611 The role of geography in human adaptation. Coop G et al. 2009 PLoS genetics
19710684 Multiple pigmentation gene polymorphisms account for a substantial proportion of risk of cutaneous malignant melanoma. Duffy DL et al. 2010 The Journal of investigative dermatology
20042077 Genetic determinants of hair and eye colours in the Scottish and Danish populations. Mengel-From J et al. 2009 BMC genetics
21052032 Sequence polymorphisms of MC1R gene and their association with depression and antidepressant response. Wu GS et al. 2011 Psychiatric genetics
21128237 Melanocortin 1 receptor and risk of cutaneous melanoma: a meta-analysis and estimates of population burden. Williams PF et al. 2011 International journal of cancer
21197618 Model-based prediction of human hair color using DNA variants. Branicki W et al. 2011 Human genetics
23110848 Human pigmentation genes under environmental selection. Sturm RA et al. 2012 Genome biology
23118974 Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations. Candille SI et al. 2012 PloS one
23744330 [Association study of MC1R gene polymorphisms with freckles in Chinese Han population from Chengdu]. Cao L et al. 2013 Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
23771755 Improved eye- and skin-color prediction based on 8 SNPs. Hart KL et al. 2013 Croatian medical journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
25945350 Variants of SCARB1 and VDR Involved in Complex Genetic Interactions May Be Implicated in the Genetic Susceptibility to Clear Cell Renal Cell Carcinoma. PoĊ›piech E et al. 2015 BioMed research international
26547235 Crowdsourced direct-to-consumer genomic analysis of a family quartet. Corpas M et al. 2015 BMC genomics
26690364 Genetic differences among ethnic groups. Huang T et al. 2015 BMC genomics
27084066 MC1R variants in Chinese Han patients with sporadic Parkinson's disease. Shi CH et al. 2016 Neurobiology of aging
27488084 Melanocortin-1 Receptor Polymorphisms and the Risk of Complicated Sepsis After Trauma: A Candidate Gene Association Study. Seaton ME et al. 2017 Shock (Augusta, Ga.)
30657907 A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect. Zorina-Lichtenwalter K et al. 2019 Human molecular genetics

Genomic regions, transcripts, and products
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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