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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.

rs1805008

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr16:89919736 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.04742 (11298/238274, GnomAD)
T=0.04632 (5816/125568, TOPMED)
T=0.05027 (5960/118548, ExAC) (+ 5 more)
T=0.0504 (1557/30916, GnomAD)
T=0.015 (73/5008, 1000G)
T=0.083 (371/4480, Estonian)
T=0.093 (357/3854, ALSPAC)
T=0.089 (330/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MC1R : Missense Variant
Publications
29 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.89919736C>T
GRCh37.p13 chr 16 NC_000016.9:g.89986144C>T
TUBB3 RefSeqGene NG_027810.1:g.2728C>T
MC1R RefSeqGene NG_012026.1:g.6858C>T
Gene: MC1R, melanocortin 1 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MC1R transcript NM_002386.3:c.478C>T R [CGG] > W [TGG] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Arg160Trp R (Arg) > W (Trp) Missense 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.

Allele: T (allele ID: 29349 )
ClinVar Accession Disease Names Clinical Significance
RCV000015381.30 Skin/hair/eye pigmentation 2, red hair/fair skin Association
RCV000015382.25 Increased analgesia from kappa-opioid receptor agonist, female-specific Affects
RCV000015383.26 OCULOCUTANEOUS ALBINISM, TYPE II, MODIFIER OF Risk-Factor
RCV000244718.1 not specified Likely-Benign
RCV000255906.1 not provided Pathogenic
RCV000356300.1 Malignant Melanoma Susceptibility Likely-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 238274 C=0.95258 T=0.04742
gnomAD - Exomes European Sub 126536 C=0.92181 T=0.07819
gnomAD - Exomes Asian Sub 47932 C=0.9965 T=0.0035
gnomAD - Exomes American Sub 33536 C=0.9917 T=0.0083
gnomAD - Exomes African Sub 15092 C=0.9875 T=0.0125
gnomAD - Exomes Ashkenazi Jewish Sub 9802 C=0.943 T=0.057
gnomAD - Exomes Other Sub 5376 C=0.960 T=0.040
TopMed Global Study-wide 125568 C=0.95368 T=0.04632
gnomAD - Genomes Global Study-wide 30916 C=0.9496 T=0.0504
gnomAD - Genomes European Sub 18460 C=0.9247 T=0.0753
gnomAD - Genomes African Sub 8718 C=0.988 T=0.012
gnomAD - Genomes East Asian Sub 1618 C=1.000 T=0.000
gnomAD - Genomes Other Sub 980 C=0.96 T=0.04
gnomAD - Genomes American Sub 838 C=0.99 T=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.95 T=0.05
1000Genomes Global Study-wide 5008 C=0.985 T=0.015
1000Genomes African Sub 1322 C=0.996 T=0.004
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.938 T=0.062
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.917 T=0.083
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.907 T=0.093
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.911 T=0.089
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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= T Note
GRCh38.p12 chr 16 NC_000016.10:g.89919736C= NC_000016.10:g.89919736C>T
GRCh37.p13 chr 16 NC_000016.9:g.89986144C= NC_000016.9:g.89986144C>T
TUBB3 RefSeqGene NG_027810.1:g.2728C= NG_027810.1:g.2728C>T
MC1R RefSeqGene NG_012026.1:g.6858C= NG_012026.1:g.6858C>T
MC1R transcript NM_002386.3:c.478C= NM_002386.3:c.478C>T
melanocyte-stimulating hormone receptor NP_002377.4:p.Arg160= NP_002377.4:p.Arg160Trp
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#.

73 SubSNP, 8 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2425921 Nov 14, 2000 (89)
2 PGA-UW-FHCRC ss4472758 Jul 03, 2002 (110)
3 SNP500CANCER ss48295621 Mar 13, 2006 (126)
4 APPLERA_GI ss48410319 Mar 13, 2006 (126)
5 PERLEGEN ss69355433 May 18, 2007 (127)
6 ILLUMINA ss74883942 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss119404118 Dec 01, 2009 (131)
8 ILLUMINA ss160463239 Dec 01, 2009 (131)
9 ILLUMINA ss172926364 Jul 04, 2010 (132)
10 1000GENOMES ss237150930 Jul 15, 2010 (132)
11 OMICIA ss244239410 May 27, 2010 (132)
12 ILLUMINA ss244285163 Jul 04, 2010 (132)
13 OMIM-CURATED-RECORDS ss275515489 Nov 24, 2010 (133)
14 ILLUMINA ss480301599 May 04, 2012 (137)
15 ILLUMINA ss480312687 May 04, 2012 (137)
16 ILLUMINA ss481068746 Sep 08, 2015 (146)
17 ILLUMINA ss484948600 May 04, 2012 (137)
18 EXOME_CHIP ss491513805 May 04, 2012 (137)
19 CLINSEQ_SNP ss491725593 May 04, 2012 (137)
20 ILLUMINA ss536992642 Sep 08, 2015 (146)
21 NHLBI-ESP ss713334841 Apr 25, 2013 (138)
22 ILLUMINA ss778841604 Aug 21, 2014 (142)
23 ILLUMINA ss780722558 Sep 08, 2015 (146)
24 ILLUMINA ss782920607 Sep 08, 2015 (146)
25 ILLUMINA ss783398386 Sep 08, 2015 (146)
26 ILLUMINA ss783883618 Aug 21, 2014 (142)
27 ILLUMINA ss832175734 Sep 08, 2015 (146)
28 ILLUMINA ss834302162 Aug 21, 2014 (142)
29 EVA-GONL ss992830732 Aug 21, 2014 (142)
30 1000GENOMES ss1357561455 Aug 21, 2014 (142)
31 EVA_GENOME_DK ss1578051494 Apr 01, 2015 (144)
32 EVA_FINRISK ss1584102414 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1635117243 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1678111276 Apr 01, 2015 (144)
35 EVA_EXAC ss1692487501 Apr 01, 2015 (144)
36 EVA_MGP ss1711441357 Apr 01, 2015 (144)
37 ILLUMINA ss1752213142 Sep 08, 2015 (146)
38 ILLUMINA ss1752213143 Sep 08, 2015 (146)
39 ILLUMINA ss1917911993 Feb 12, 2016 (147)
40 ILLUMINA ss1946424254 Feb 12, 2016 (147)
41 ILLUMINA ss1959711643 Feb 12, 2016 (147)
42 JJLAB ss2028926298 Sep 14, 2016 (149)
43 ILLUMINA ss2095070738 Dec 20, 2016 (150)
44 USC_VALOUEV ss2157367879 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2214824195 Dec 20, 2016 (150)
46 TOPMED ss2379650267 Dec 20, 2016 (150)
47 ILLUMINA ss2633363343 Nov 08, 2017 (151)
48 GNOMAD ss2742271371 Nov 08, 2017 (151)
49 GNOMAD ss2749635808 Nov 08, 2017 (151)
50 GNOMAD ss2946702241 Nov 08, 2017 (151)
51 AFFY ss2985080457 Nov 08, 2017 (151)
52 SWEGEN ss3015041398 Nov 08, 2017 (151)
53 ILLUMINA ss3021742098 Nov 08, 2017 (151)
54 TOPMED ss3255026653 Nov 08, 2017 (151)
55 CSHL ss3351606491 Nov 08, 2017 (151)
56 ILLUMINA ss3625702176 Oct 12, 2018 (152)
57 ILLUMINA ss3627602955 Oct 12, 2018 (152)
58 ILLUMINA ss3627602956 Oct 12, 2018 (152)
59 ILLUMINA ss3631346738 Oct 12, 2018 (152)
60 ILLUMINA ss3633838992 Oct 12, 2018 (152)
61 ILLUMINA ss3634658692 Oct 12, 2018 (152)
62 ILLUMINA ss3634658693 Oct 12, 2018 (152)
63 ILLUMINA ss3635527017 Oct 12, 2018 (152)
64 ILLUMINA ss3636350096 Oct 12, 2018 (152)
65 ILLUMINA ss3637278512 Oct 12, 2018 (152)
66 ILLUMINA ss3638143984 Oct 12, 2018 (152)
67 ILLUMINA ss3640366012 Oct 12, 2018 (152)
68 ILLUMINA ss3640366013 Oct 12, 2018 (152)
69 ILLUMINA ss3643123678 Oct 12, 2018 (152)
70 ILLUMINA ss3644677335 Oct 12, 2018 (152)
71 ILLUMINA ss3652154500 Oct 12, 2018 (152)
72 ILLUMINA ss3652154501 Oct 12, 2018 (152)
73 ILLUMINA ss3653852554 Oct 12, 2018 (152)
74 1000Genomes NC_000016.9 - 89986144 Oct 12, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 89986144 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000016.9 - 89986144 Oct 12, 2018 (152)
77 ExAC NC_000016.9 - 89986144 Oct 12, 2018 (152)
78 gnomAD - Genomes NC_000016.9 - 89986144 Oct 12, 2018 (152)
79 gnomAD - Exomes NC_000016.9 - 89986144 Oct 12, 2018 (152)
80 TopMed NC_000016.10 - 89919736 Oct 12, 2018 (152)
81 UK 10K study - Twins NC_000016.9 - 89986144 Oct 12, 2018 (152)
82 ClinVar RCV000015381.30 Oct 12, 2018 (152)
83 ClinVar RCV000015382.25 Oct 12, 2018 (152)
84 ClinVar RCV000015383.26 Oct 12, 2018 (152)
85 ClinVar RCV000244718.1 Oct 12, 2018 (152)
86 ClinVar RCV000255906.1 Oct 12, 2018 (152)
87 ClinVar RCV000356300.1 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)
rs3212382 Dec 16, 2002 (110)
rs386545682 Aug 06, 2014 (136)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss480301599, ss491725593, ss3643123678 NC_000016.8:88513644:C= NC_000016.10:89919735:C= (self)
70762818, 39253512, 27757447, 2907957, 80403768, 9114141, 39253512, ss237150930, ss480312687, ss481068746, ss484948600, ss491513805, ss536992642, ss713334841, ss778841604, ss780722558, ss782920607, ss783398386, ss783883618, ss832175734, ss834302162, ss992830732, ss1357561455, ss1578051494, ss1584102414, ss1635117243, ss1678111276, ss1692487501, ss1711441357, ss1752213142, ss1752213143, ss1917911993, ss1946424254, ss1959711643, ss2028926298, ss2095070738, ss2157367879, ss2379650267, ss2633363343, ss2742271371, ss2749635808, ss2946702241, ss2985080457, ss3015041398, ss3021742098, ss3351606491, ss3625702176, ss3627602955, ss3627602956, ss3631346738, ss3633838992, ss3634658692, ss3634658693, ss3635527017, ss3636350096, ss3637278512, ss3638143984, ss3640366012, ss3640366013, ss3644677335, ss3652154500, ss3652154501, ss3653852554 NC_000016.9:89986143:C= NC_000016.10:89919735:C= (self)
151103895, ss244239410, ss275515489, ss2214824195, ss3255026653 NC_000016.10:89919735:C= NC_000016.10:89919735:C= (self)
ss2425921, ss4472758, ss48295621, ss48410319, ss69355433, ss74883942, ss119404118, ss160463239, ss172926364, ss244285163 NT_010542.15:1546760:C= NC_000016.10:89919735:C= (self)
ss480301599, ss491725593, ss3643123678 NC_000016.8:88513644:C>T NC_000016.10:89919735:C>T (self)
70762818, 39253512, 27757447, 2907957, 80403768, 9114141, 39253512, ss237150930, ss480312687, ss481068746, ss484948600, ss491513805, ss536992642, ss713334841, ss778841604, ss780722558, ss782920607, ss783398386, ss783883618, ss832175734, ss834302162, ss992830732, ss1357561455, ss1578051494, ss1584102414, ss1635117243, ss1678111276, ss1692487501, ss1711441357, ss1752213142, ss1752213143, ss1917911993, ss1946424254, ss1959711643, ss2028926298, ss2095070738, ss2157367879, ss2379650267, ss2633363343, ss2742271371, ss2749635808, ss2946702241, ss2985080457, ss3015041398, ss3021742098, ss3351606491, ss3625702176, ss3627602955, ss3627602956, ss3631346738, ss3633838992, ss3634658692, ss3634658693, ss3635527017, ss3636350096, ss3637278512, ss3638143984, ss3640366012, ss3640366013, ss3644677335, ss3652154500, ss3652154501, ss3653852554 NC_000016.9:89986143:C>T NC_000016.10:89919735:C>T (self)
RCV000015381.30, RCV000015382.25, RCV000015383.26, RCV000244718.1, RCV000255906.1, RCV000356300.1, 151103895, ss244239410, ss275515489, ss2214824195, ss3255026653 NC_000016.10:89919735:C>T NC_000016.10:89919735:C>T (self)
ss2425921, ss4472758, ss48295621, ss48410319, ss69355433, ss74883942, ss119404118, ss160463239, ss172926364, ss244285163 NT_010542.15:1546760:C>T NC_000016.10:89919735:C>T (self)
Help

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

29 citations for rs1805008
PMID Title Author Year Journal
9665397 Melanocortin 1 receptor variants in an Irish population. Smith R et al. 1998 The Journal of investigative dermatology
12876664 MC1R mutations modify the classic phenotype of oculocutaneous albinism type 2 (OCA2). King RA et al. 2003 American journal of human genetics
15994880 Melanocortin-1 receptor gene variants affect pain and mu-opioid analgesia in mice and humans. Mogil JS et al. 2005 Journal of medical genetics
17616515 Receptor function, dominant negative activity and phenotype correlations for MC1R variant alleles. Beaumont KA et al. 2007 Human molecular genetics
17952075 Genetic determinants of hair, eye and skin pigmentation in Europeans. Sulem P et al. 2007 Nature genetics
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
18392143 Interactions between SNP alleles at multiple loci contribute to skin color differences between caucasoid and mongoloid subjects. Anno S et al. 2008 International journal of biological sciences
19320745 Contribution of genetic factors for melanoma susceptibility in sporadic US melanoma patients. Council ML et al. 2009 Experimental dermatology
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
20158590 Predicting phenotype from genotype: normal pigmentation. Valenzuela RK et al. 2010 Journal of forensic sciences
20546537 Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis. Gerstenblith MR et al. 2010 Pigment cell & melanoma research
20585627 Web-based, participant-driven studies yield novel genetic associations for common traits. Eriksson N et al. 2010 PLoS genetics
20670983 The Multiple Sclerosis Severity Score: associations with MC1R single nucleotide polymorphisms and host response to ultraviolet radiation. Strange RC et al. 2010 Multiple sclerosis (Houndmills, Basingstoke, England)
21197618 Model-based prediction of human hair color using DNA variants. Branicki W et al. 2011 Human genetics
21829225 People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population. Winney B et al. 2012 European journal of human genetics
21926416 Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Amos CI et al. 2011 Human molecular genetics
22140526 Detecting low frequent loss-of-function alleles in genome wide association studies with red hair color as example. Liu F et al. 2011 PloS one
24086514 Association of polymorphisms in pharmacogenetic candidate genes (OPRD1, GAL, ABCB1, OPRM1) with opioid dependence in European population: a case-control study. Beer B et al. 2013 PloS one
24439955 Susceptibility loci for pigmentation and melanoma in relation to Parkinson's disease. Dong J et al. 2014 Neurobiology of aging
24809478 Implications of the admixture process in skin color molecular assessment. Cerqueira CC et al. 2014 PloS one
25631192 The MC1R melanoma risk variant p.R160W is associated with Parkinson disease. Tell-Marti G et al. 2015 Annals of neurology
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. Pośpiech E et al. 2015 BioMed research international
26389780 Reply. Tell-Martí G et al. 2016 Annals of neurology
26389967 Is the MC1R variant p.R160W associated with Parkinson's? Lubbe SJ et al. 2016 Annals of neurology
26547235 Crowdsourced direct-to-consumer genomic analysis of a family quartet. Corpas M et al. 2015 BMC genomics
28242083 Association of five SNPs with human hair colour in the Polish population. Siewierska-Górska A et al. 2017 Homo
29518100 Associations between sun sensitive pigmentary genes and serum prostate specific antigen levels. Nair-Shalliker V et al. 2018 PloS one

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.post63+3f7b20b