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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.

rs1805006

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:89919510 (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>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00613 (770/125568, TOPMED)
A=0.0020 (158/78686, PAGE_STUDY)
A=0.0043 (136/31382, GnomAD) (+ 5 more)
A=0.003 (13/5008, 1000G)
A=0.000 (1/4480, Estonian)
A=0.010 (39/3854, ALSPAC)
A=0.008 (29/3708, TWINSUK)
A=0.01 (4/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MC1R : Missense Variant
Publications
12 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.89919510C>A
GRCh38.p12 chr 16 NC_000016.10:g.89919510C>G
GRCh37.p13 chr 16 NC_000016.9:g.89985918C>A
GRCh37.p13 chr 16 NC_000016.9:g.89985918C>G
TUBB3 RefSeqGene NG_027810.1:g.2502C>A
TUBB3 RefSeqGene NG_027810.1:g.2502C>G
MC1R RefSeqGene NG_012026.1:g.6632C>A
MC1R RefSeqGene NG_012026.1:g.6632C>G
Gene: MC1R, melanocortin 1 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MC1R transcript NM_002386.3:c.252C>A D [GAC] > E [GAA] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp84Glu D (Asp) > E (Glu) Missense Variant
MC1R transcript NM_002386.3:c.252C>G D [GAC] > E [GAG] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp84Glu D (Asp) > E (Glu) 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: A (allele ID: 29348 )
ClinVar Accession Disease Names Clinical Significance
RCV000015380.8 Cutaneous malignant melanoma 5 Benign
RCV000375124.1 Malignant Melanoma Susceptibility Likely-Benign
RCV000413549.1 not provided Likely-Pathogenic
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 C=0.99387 A=0.00613
The PAGE Study Global Study-wide 78686 C=0.9980 A=0.0020
The PAGE Study AfricanAmerican Sub 32502 C=0.9975 A=0.0025
The PAGE Study Mexican Sub 10810 C=0.9975 A=0.0025
The PAGE Study Asian Sub 8316 C=1.000 A=0.000
The PAGE Study PuertoRican Sub 7918 C=0.998 A=0.002
The PAGE Study NativeHawaiian Sub 4534 C=0.999 A=0.001
The PAGE Study Cuban Sub 4230 C=0.997 A=0.003
The PAGE Study Dominican Sub 3828 C=0.999 A=0.001
The PAGE Study CentralAmerican Sub 2450 C=0.998 A=0.002
The PAGE Study SouthAmerican Sub 1982 C=0.995 A=0.005
The PAGE Study NativeAmerican Sub 1260 C=0.998 A=0.002
The PAGE Study SouthAsian Sub 856 C=1.00 A=0.00
gnomAD - Genomes Global Study-wide 31382 C=0.9957 A=0.0043
gnomAD - Genomes European Sub 18896 C=0.9938 A=0.0062
gnomAD - Genomes African Sub 8702 C=0.998 A=0.002
gnomAD - Genomes East Asian Sub 1558 C=1.000 A=0.000
gnomAD - Genomes Other Sub 1088 C=0.998 A=0.002
gnomAD - Genomes American Sub 848 C=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 A=0.00
1000Genomes Global Study-wide 5008 C=0.997 A=0.003
1000Genomes African Sub 1322 C=0.999 A=0.001
1000Genomes East Asian Sub 1008 C=1.000 A=0.000
1000Genomes Europe Sub 1006 C=0.990 A=0.010
1000Genomes South Asian Sub 978 C=1.00 A=0.00
1000Genomes American Sub 694 C=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.990 A=0.010
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.992 A=0.008
Northern Sweden ACPOP Study-wide 600 C=0.99 A=0.01
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= A G Note
GRCh38.p12 chr 16 NC_000016.10:g.89...

NC_000016.10:g.89919510=

NC_000016.10:g.89...

NC_000016.10:g.89919510C>A

NC_000016.10:g.89...

NC_000016.10:g.89919510C>G

GRCh37.p13 chr 16 NC_000016.9:g.899...

NC_000016.9:g.89985918=

NC_000016.9:g.899...

NC_000016.9:g.89985918C>A

NC_000016.9:g.899...

NC_000016.9:g.89985918C>G

TUBB3 RefSeqGene NG_027810.1:g.2502= NG_027810.1:g.250...

NG_027810.1:g.2502C>A

NG_027810.1:g.250...

NG_027810.1:g.2502C>G

MC1R RefSeqGene NG_012026.1:g.6632= NG_012026.1:g.663...

NG_012026.1:g.6632C>A

NG_012026.1:g.663...

NG_012026.1:g.6632C>G

MC1R transcript NM_002386.3:c.252= NM_002386.3:c.252C>A NM_002386.3:c.252C>G
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp84= NP_002377.4:p.Asp...

NP_002377.4:p.Asp84Glu

NP_002377.4:p.Asp...

NP_002377.4:p.Asp84Glu

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#.

70 SubSNP, 12 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2425919 Nov 14, 2000 (89)
2 SNP500CANCER ss48295619 Mar 14, 2006 (126)
3 ILLUMINA ss160463238 Dec 01, 2009 (131)
4 OMICIA ss244239426 May 27, 2010 (132)
5 ILLUMINA ss244285162 Jul 04, 2010 (132)
6 1000GENOMES ss339495613 May 09, 2011 (134)
7 ILLUMINA ss480301595 May 04, 2012 (137)
8 ILLUMINA ss480312683 May 04, 2012 (137)
9 ILLUMINA ss481068742 Sep 08, 2015 (146)
10 ILLUMINA ss484948598 May 04, 2012 (137)
11 EXOME_CHIP ss491513791 May 04, 2012 (137)
12 CLINSEQ_SNP ss491725584 May 04, 2012 (137)
13 ILLUMINA ss536992641 Sep 08, 2015 (146)
14 NHLBI-ESP ss713340290 Apr 25, 2013 (138)
15 ILLUMINA ss778697572 Sep 08, 2015 (146)
16 ILLUMINA ss780722549 Sep 08, 2015 (146)
17 ILLUMINA ss782920606 Sep 08, 2015 (146)
18 ILLUMINA ss783398377 Sep 08, 2015 (146)
19 ILLUMINA ss783883617 Sep 08, 2015 (146)
20 ILLUMINA ss832175733 Sep 08, 2015 (146)
21 ILLUMINA ss834156427 Sep 08, 2015 (146)
22 EVA-GONL ss992830726 Aug 21, 2014 (142)
23 1000GENOMES ss1357561429 Aug 21, 2014 (142)
24 EVA_UK10K_ALSPAC ss1635117231 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1678111264 Apr 01, 2015 (144)
26 EVA_EXAC ss1692487428 Apr 01, 2015 (144)
27 EVA_EXAC ss1692487429 Apr 01, 2015 (144)
28 EVA_DECODE ss1696872305 Apr 01, 2015 (144)
29 ILLUMINA ss1752213131 Sep 08, 2015 (146)
30 ILLUMINA ss1752213132 Sep 08, 2015 (146)
31 ILLUMINA ss1917911983 Feb 12, 2016 (147)
32 ILLUMINA ss1946424244 Feb 12, 2016 (147)
33 ILLUMINA ss1959711630 Feb 12, 2016 (147)
34 JJLAB ss2028926294 Sep 14, 2016 (149)
35 HUMAN_LONGEVITY ss2214824158 Dec 20, 2016 (150)
36 TOPMED ss2379650225 Dec 20, 2016 (150)
37 ILLUMINA ss2633363336 Nov 08, 2017 (151)
38 GNOMAD ss2742271266 Nov 08, 2017 (151)
39 GNOMAD ss2749635761 Nov 08, 2017 (151)
40 GNOMAD ss2946702194 Nov 08, 2017 (151)
41 AFFY ss2985080444 Nov 08, 2017 (151)
42 SWEGEN ss3015041386 Nov 08, 2017 (151)
43 ILLUMINA ss3021742084 Nov 08, 2017 (151)
44 TOPMED ss3255026567 Nov 08, 2017 (151)
45 CSHL ss3351606487 Nov 08, 2017 (151)
46 ILLUMINA ss3625702174 Oct 12, 2018 (152)
47 ILLUMINA ss3627602936 Oct 12, 2018 (152)
48 ILLUMINA ss3627602937 Oct 12, 2018 (152)
49 ILLUMINA ss3631346730 Oct 12, 2018 (152)
50 ILLUMINA ss3633132161 Oct 12, 2018 (152)
51 ILLUMINA ss3633838989 Oct 12, 2018 (152)
52 ILLUMINA ss3634658679 Oct 12, 2018 (152)
53 ILLUMINA ss3634658680 Oct 12, 2018 (152)
54 ILLUMINA ss3636350092 Oct 12, 2018 (152)
55 ILLUMINA ss3637278509 Oct 12, 2018 (152)
56 ILLUMINA ss3640365999 Oct 12, 2018 (152)
57 ILLUMINA ss3640366000 Oct 12, 2018 (152)
58 ILLUMINA ss3644677325 Oct 12, 2018 (152)
59 ILLUMINA ss3652154482 Oct 12, 2018 (152)
60 ILLUMINA ss3653852541 Oct 12, 2018 (152)
61 EGCUT_WGS ss3682019183 Jul 13, 2019 (153)
62 EVA_DECODE ss3699905740 Jul 13, 2019 (153)
63 ILLUMINA ss3725591482 Jul 13, 2019 (153)
64 ACPOP ss3741791955 Jul 13, 2019 (153)
65 ILLUMINA ss3744436932 Jul 13, 2019 (153)
66 ILLUMINA ss3744959042 Jul 13, 2019 (153)
67 ILLUMINA ss3744959043 Jul 13, 2019 (153)
68 PAGE_CC ss3771903544 Jul 13, 2019 (153)
69 ILLUMINA ss3772457148 Jul 13, 2019 (153)
70 ILLUMINA ss3772457149 Jul 13, 2019 (153)
71 1000Genomes NC_000016.9 - 89985918 Oct 12, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 89985918 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000016.9 - 89985918 Oct 12, 2018 (152)
74 ExAC

Submission ignored due to conflicting rows:
Row 2907883 (NC_000016.9:89985917:C:C 119386/120024, NC_000016.9:89985917:C:A 638/120024)
Row 2907884 (NC_000016.9:89985917:C:C 120023/120024, NC_000016.9:89985917:C:G 1/120024)

- Oct 12, 2018 (152)
75 ExAC

Submission ignored due to conflicting rows:
Row 2907883 (NC_000016.9:89985917:C:C 119386/120024, NC_000016.9:89985917:C:A 638/120024)
Row 2907884 (NC_000016.9:89985917:C:C 120023/120024, NC_000016.9:89985917:C:G 1/120024)

- Oct 12, 2018 (152)
76 gnomAD - Genomes NC_000016.9 - 89985918 Jul 13, 2019 (153)
77 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11564141 (NC_000016.9:89985917:C:C 247400/248704, NC_000016.9:89985917:C:A 1304/248704)
Row 11564142 (NC_000016.9:89985917:C:C 248703/248704, NC_000016.9:89985917:C:G 1/248704)

- Jul 13, 2019 (153)
78 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11564141 (NC_000016.9:89985917:C:C 247400/248704, NC_000016.9:89985917:C:A 1304/248704)
Row 11564142 (NC_000016.9:89985917:C:C 248703/248704, NC_000016.9:89985917:C:G 1/248704)

- Jul 13, 2019 (153)
79 Northern Sweden NC_000016.9 - 89985918 Jul 13, 2019 (153)
80 The PAGE Study NC_000016.10 - 89919510 Jul 13, 2019 (153)
81 TopMed NC_000016.10 - 89919510 Oct 12, 2018 (152)
82 UK 10K study - Twins NC_000016.9 - 89985918 Oct 12, 2018 (152)
83 ClinVar RCV000015380.8 Oct 12, 2018 (152)
84 ClinVar RCV000375124.1 Oct 12, 2018 (152)
85 ClinVar RCV000413549.1 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss480301595, ss491725584, ss1696872305 NC_000016.8:88513418:C:A NC_000016.10:89919509:C:A (self)
70762792, 39253500, 27757431, 193093814, 15076820, 39253500, ss339495613, ss480312683, ss481068742, ss484948598, ss491513791, ss536992641, ss713340290, ss778697572, ss780722549, ss782920606, ss783398377, ss783883617, ss832175733, ss834156427, ss992830726, ss1357561429, ss1635117231, ss1678111264, ss1692487428, ss1752213131, ss1752213132, ss1917911983, ss1946424244, ss1959711630, ss2028926294, ss2379650225, ss2633363336, ss2742271266, ss2749635761, ss2946702194, ss2985080444, ss3015041386, ss3021742084, ss3351606487, ss3625702174, ss3627602936, ss3627602937, ss3631346730, ss3633132161, ss3633838989, ss3634658679, ss3634658680, ss3636350092, ss3637278509, ss3640365999, ss3640366000, ss3644677325, ss3652154482, ss3653852541, ss3682019183, ss3741791955, ss3744436932, ss3744959042, ss3744959043, ss3772457148, ss3772457149 NC_000016.9:89985917:C:A NC_000016.10:89919509:C:A (self)
RCV000015380.8, RCV000375124.1, RCV000413549.1, 1125013, 151103818, ss244239426, ss2214824158, ss3255026567, ss3699905740, ss3725591482, ss3771903544 NC_000016.10:89919509:C:A NC_000016.10:89919509:C:A (self)
ss2425919, ss48295619, ss160463238, ss244285162 NT_010542.15:1546534:C:A NC_000016.10:89919509:C:A (self)
ss1692487429, ss2742271266 NC_000016.9:89985917:C:G NC_000016.10:89919509:C:G (self)
Help

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

12 citations for rs1805006
PMID Title Author Year Journal
8894704 The Asp84Glu variant of the melanocortin 1 receptor (MC1R) is associated with melanoma. Valverde P et al. 1996 Human molecular genetics
14757863 Melanocortin 1 receptor (MC1R) gene variants may increase the risk of melanoma in France independently of clinical risk factors and UV exposure. Matichard E et al. 2004 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
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
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
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
21926416 Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Amos CI et al. 2011 Human molecular genetics
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
26848990 Biochip-Based Genotyping Assay for Detection of Polymorphisms in Pigmentation Genes Associated with Cutaneous Melanoma. Fesenko DO et al. 2016 Genetic testing and molecular biomarkers

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