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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.

rs1805009

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:89920138 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.01239 (1556/125568, TOPMED)
C=0.0057 (446/78688, PAGE_STUDY)
C=0.0097 (305/31376, GnomAD) (+ 5 more)
C=0.003 (17/5008, 1000G)
C=0.003 (15/4480, Estonian)
C=0.022 (85/3854, ALSPAC)
C=0.022 (82/3708, TWINSUK)
C=0.02 (10/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MC1R : Missense Variant
TUBB3 : 2KB Upstream Variant
Publications
14 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.89920138G>A
GRCh38.p12 chr 16 NC_000016.10:g.89920138G>C
GRCh37.p13 chr 16 NC_000016.9:g.89986546G>A
GRCh37.p13 chr 16 NC_000016.9:g.89986546G>C
TUBB3 RefSeqGene NG_027810.1:g.3130G>A
TUBB3 RefSeqGene NG_027810.1:g.3130G>C
MC1R RefSeqGene NG_012026.1:g.7260G>A
MC1R RefSeqGene NG_012026.1:g.7260G>C
Gene: TUBB3, tubulin beta 3 class III (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TUBB3 transcript variant 2 NM_001197181.2:c. N/A Upstream Transcript Variant
TUBB3 transcript variant 1 NM_006086.4:c. N/A N/A
Gene: MC1R, melanocortin 1 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MC1R transcript NM_002386.3:c.880G>A D [GAC] > N [AAC] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp294Asn D (Asp) > N (Asn) Missense Variant
MC1R transcript NM_002386.3:c.880G>C D [GAC] > H [CAC] Coding Sequence Variant
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp294His D (Asp) > H (His) 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: C (allele ID: 29346 )
ClinVar Accession Disease Names Clinical Significance
RCV000015377.26 Skin/hair/eye pigmentation 2, red hair/fair skin Association
RCV000231551.4 Cutaneous malignant melanoma 5 Benign
RCV000243405.1 not specified Likely-Benign
RCV000299359.1 Malignant Melanoma Susceptibility Likely-Benign
RCV000347221.2 not provided Pathogenic
RCV000662303.1 Tyrosinase-positive oculocutaneous albinism 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 G=0.98761 C=0.01239
The PAGE Study Global Study-wide 78688 G=0.9943 C=0.0057
The PAGE Study AfricanAmerican Sub 32510 G=0.9958 C=0.0042
The PAGE Study Mexican Sub 10806 G=0.9916 C=0.0084
The PAGE Study Asian Sub 8318 G=1.000 C=0.000
The PAGE Study PuertoRican Sub 7918 G=0.988 C=0.012
The PAGE Study NativeHawaiian Sub 4532 G=0.998 C=0.002
The PAGE Study Cuban Sub 4228 G=0.988 C=0.012
The PAGE Study Dominican Sub 3828 G=0.997 C=0.003
The PAGE Study CentralAmerican Sub 2450 G=0.993 C=0.007
The PAGE Study SouthAmerican Sub 1982 G=0.991 C=0.009
The PAGE Study NativeAmerican Sub 1260 G=0.990 C=0.010
The PAGE Study SouthAsian Sub 856 G=1.00 C=0.00
gnomAD - Genomes Global Study-wide 31376 G=0.9903 C=0.0097
gnomAD - Genomes European Sub 18892 G=0.9864 C=0.0136
gnomAD - Genomes African Sub 8706 G=0.996 C=0.004
gnomAD - Genomes East Asian Sub 1554 G=1.000 C=0.000
gnomAD - Genomes Other Sub 1088 G=0.991 C=0.009
gnomAD - Genomes American Sub 846 G=1.00 C=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.00 C=0.00
1000Genomes Global Study-wide 5008 G=0.997 C=0.003
1000Genomes African Sub 1322 G=0.998 C=0.002
1000Genomes East Asian Sub 1008 G=1.000 C=0.000
1000Genomes Europe Sub 1006 G=0.992 C=0.008
1000Genomes South Asian Sub 978 G=1.00 C=0.00
1000Genomes American Sub 694 G=0.99 C=0.01
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.997 C=0.003
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.978 C=0.022
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.978 C=0.022
Northern Sweden ACPOP Study-wide 600 G=0.98 C=0.02
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 C Note
GRCh38.p12 chr 16 NC_000016.10:g.89...

NC_000016.10:g.89920138=

NC_000016.10:g.89...

NC_000016.10:g.89920138G>A

NC_000016.10:g.89...

NC_000016.10:g.89920138G>C

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

NC_000016.9:g.89986546=

NC_000016.9:g.899...

NC_000016.9:g.89986546G>A

NC_000016.9:g.899...

NC_000016.9:g.89986546G>C

TUBB3 RefSeqGene NG_027810.1:g.3130= NG_027810.1:g.313...

NG_027810.1:g.3130G>A

NG_027810.1:g.313...

NG_027810.1:g.3130G>C

MC1R RefSeqGene NG_012026.1:g.7260= NG_012026.1:g.726...

NG_012026.1:g.7260G>A

NG_012026.1:g.726...

NG_012026.1:g.7260G>C

MC1R transcript NM_002386.3:c.880= NM_002386.3:c.880G>A NM_002386.3:c.880G>C
melanocyte-stimulating hormone receptor NP_002377.4:p.Asp...

NP_002377.4:p.Asp294=

NP_002377.4:p.Asp...

NP_002377.4:p.Asp294Asn

NP_002377.4:p.Asp...

NP_002377.4:p.Asp294His

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#.

36 SubSNP, 12 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2425922 Nov 14, 2000 (89)
2 SNP500CANCER ss105440256 Feb 06, 2009 (130)
3 OMICIA ss244239406 May 27, 2010 (132)
4 OMIM-CURATED-RECORDS ss275515486 Nov 24, 2010 (133)
5 1000GENOMES ss464764753 Sep 17, 2011 (135)
6 EXOME_CHIP ss491513815 May 04, 2012 (137)
7 CLINSEQ_SNP ss491725601 May 04, 2012 (137)
8 NHLBI-ESP ss713334896 Apr 25, 2013 (138)
9 EVA-GONL ss992830737 Aug 21, 2014 (142)
10 1000GENOMES ss1357561492 Aug 21, 2014 (142)
11 EVA_FINRISK ss1584102418 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1635117263 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1678111296 Apr 01, 2015 (144)
14 EVA_EXAC ss1692487669 Apr 01, 2015 (144)
15 EVA_EXAC ss1692487670 Apr 01, 2015 (144)
16 EVA_DECODE ss1696872320 Apr 01, 2015 (144)
17 EVA_MGP ss1711441363 Apr 01, 2015 (144)
18 ILLUMINA ss1959711655 Feb 12, 2016 (147)
19 JJLAB ss2028926303 Sep 14, 2016 (149)
20 USC_VALOUEV ss2157367883 Dec 20, 2016 (150)
21 HUMAN_LONGEVITY ss2214824269 Dec 20, 2016 (150)
22 TOPMED ss2379650333 Dec 20, 2016 (150)
23 GNOMAD ss2742271554 Nov 08, 2017 (151)
24 GNOMAD ss2749635887 Nov 08, 2017 (151)
25 GNOMAD ss2946702320 Nov 08, 2017 (151)
26 AFFY ss2985080468 Nov 08, 2017 (151)
27 SWEGEN ss3015041409 Nov 08, 2017 (151)
28 ILLUMINA ss3021742114 Nov 08, 2017 (151)
29 TOPMED ss3255026822 Nov 08, 2017 (151)
30 ILLUMINA ss3652154517 Oct 12, 2018 (152)
31 ILLUMINA ss3653852565 Oct 12, 2018 (152)
32 EGCUT_WGS ss3682019210 Jul 13, 2019 (153)
33 EVA_DECODE ss3699905765 Jul 13, 2019 (153)
34 ILLUMINA ss3725591509 Jul 13, 2019 (153)
35 ACPOP ss3741791966 Jul 13, 2019 (153)
36 PAGE_CC ss3771903567 Jul 13, 2019 (153)
37 1000Genomes NC_000016.9 - 89986546 Oct 12, 2018 (152)
38 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 89986546 Oct 12, 2018 (152)
39 Genetic variation in the Estonian population NC_000016.9 - 89986546 Oct 12, 2018 (152)
40 ExAC

Submission ignored due to conflicting rows:
Row 2908142 (NC_000016.9:89986545:G:G 119484/120516, NC_000016.9:89986545:G:C 1032/120516)
Row 2908143 (NC_000016.9:89986545:G:G 120515/120516, NC_000016.9:89986545:G:A 1/120516)

- Oct 12, 2018 (152)
41 ExAC

Submission ignored due to conflicting rows:
Row 2908142 (NC_000016.9:89986545:G:G 119484/120516, NC_000016.9:89986545:G:C 1032/120516)
Row 2908143 (NC_000016.9:89986545:G:G 120515/120516, NC_000016.9:89986545:G:A 1/120516)

- Oct 12, 2018 (152)
42 gnomAD - Genomes NC_000016.9 - 89986546 Jul 13, 2019 (153)
43 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11564488 (NC_000016.9:89986545:G:G 249065/249066, NC_000016.9:89986545:G:A 1/249066)
Row 11564489 (NC_000016.9:89986545:G:G 246803/249066, NC_000016.9:89986545:G:C 2263/249066)

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

Submission ignored due to conflicting rows:
Row 11564488 (NC_000016.9:89986545:G:G 249065/249066, NC_000016.9:89986545:G:A 1/249066)
Row 11564489 (NC_000016.9:89986545:G:G 246803/249066, NC_000016.9:89986545:G:C 2263/249066)

- Jul 13, 2019 (153)
45 Northern Sweden NC_000016.9 - 89986546 Jul 13, 2019 (153)
46 The PAGE Study NC_000016.10 - 89920138 Jul 13, 2019 (153)
47 TopMed NC_000016.10 - 89920138 Oct 12, 2018 (152)
48 UK 10K study - Twins NC_000016.9 - 89986546 Oct 12, 2018 (152)
49 ClinVar RCV000015377.26 Oct 12, 2018 (152)
50 ClinVar RCV000231551.4 Oct 12, 2018 (152)
51 ClinVar RCV000243405.1 Oct 12, 2018 (152)
52 ClinVar RCV000299359.1 Oct 12, 2018 (152)
53 ClinVar RCV000347221.2 Oct 12, 2018 (152)
54 ClinVar RCV000662303.1 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
ss1692487670, ss2742271554 NC_000016.9:89986545:G:A NC_000016.10:89920137:G:A (self)
ss491725601, ss1696872320 NC_000016.8:88514046:G:C NC_000016.10:89920137:G:C (self)
70762856, 39253532, 27757458, 193093945, 15076831, 39253532, ss464764753, ss491513815, ss713334896, ss992830737, ss1357561492, ss1584102418, ss1635117263, ss1678111296, ss1692487669, ss1711441363, ss1959711655, ss2028926303, ss2157367883, ss2379650333, ss2742271554, ss2749635887, ss2946702320, ss2985080468, ss3015041409, ss3021742114, ss3652154517, ss3653852565, ss3682019210, ss3741791966 NC_000016.9:89986545:G:C NC_000016.10:89920137:G:C (self)
RCV000015377.26, RCV000231551.4, RCV000243405.1, RCV000299359.1, RCV000347221.2, RCV000662303.1, 1125036, 151104048, ss244239406, ss275515486, ss2214824269, ss3255026822, ss3699905765, ss3725591509, ss3771903567 NC_000016.10:89920137:G:C NC_000016.10:89920137:G:C (self)
ss2425922, ss105440256 NT_010542.15:1547162:G:C NC_000016.10:89920137:G:C (self)
Help

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

14 citations for rs1805009
PMID Title Author Year Journal
7581459 Variants of the melanocyte-stimulating hormone receptor gene are associated with red hair and fair skin in humans. Valverde P et al. 1995 Nature genetics
11179997 Melanocortin-1 receptor genotype is a risk factor for basal and squamous cell carcinoma. Box NF et al. 2001 The Journal of investigative dermatology
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
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
24809478 Implications of the admixture process in skin color molecular assessment. Cerqueira CC et al. 2014 PloS one
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
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
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