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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.

rs2424984

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr20:34262569 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.29566 (37126/125568, TOPMED)
C=0.2887 (9035/31300, GnomAD)
C=0.326 (1634/5008, 1000G) (+ 4 more)
C=0.141 (632/4480, Estonian)
C=0.104 (399/3854, ALSPAC)
C=0.101 (374/3708, TWINSUK)
C=0.12 (69/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AHCY : Intron Variant
ASIP : Intron Variant
Publications
1 citation
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 20 NC_000020.11:g.34262569T>A
GRCh38.p12 chr 20 NC_000020.11:g.34262569T>C
GRCh37.p13 chr 20 NC_000020.10:g.32850375T>A
GRCh37.p13 chr 20 NC_000020.10:g.32850375T>C
ASIP RefSeqGene NG_011439.1:g.7205T>A
ASIP RefSeqGene NG_011439.1:g.7205T>C
Gene: ASIP, agouti signaling protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ASIP transcript NM_001672.2:c. N/A Intron Variant
ASIP transcript variant X1 XM_005260412.3:c. N/A Intron Variant
ASIP transcript variant X2 XM_011528820.2:c. N/A Intron Variant
ASIP transcript variant X3 XM_011528821.1:c. N/A Intron Variant
Gene: AHCY, adenosylhomocysteinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AHCY transcript variant 1 NM_000687.4:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant 2 NM_001161766.1:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant 4 NM_001322084.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant 5 NM_001322085.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant 3 NM_001322086.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant 6 NM_001362750.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X2 XM_011528657.2:c. N/A Intron Variant
AHCY transcript variant X6 XM_005260317.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X1 XM_011528656.3:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X3 XM_011528658.3:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X7 XM_011528659.1:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X5 XM_017027709.2:c. N/A Genic Downstream Transcript Variant
AHCY transcript variant X8 XM_017027710.2:c. N/A Genic Downstream Transcript 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.

Not Reported in ClinVar
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 T=0.70434 C=0.29566
gnomAD - Genomes Global Study-wide 31300 T=0.7113 C=0.2887
gnomAD - Genomes European Sub 18868 T=0.8791 C=0.1209
gnomAD - Genomes African Sub 8680 T=0.299 C=0.701
gnomAD - Genomes East Asian Sub 1532 T=0.766 C=0.234
gnomAD - Genomes Other Sub 1084 T=0.837 C=0.163
gnomAD - Genomes American Sub 848 T=0.90 C=0.10
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.84 C=0.16
1000Genomes Global Study-wide 5008 T=0.674 C=0.326
1000Genomes African Sub 1322 T=0.199 C=0.801
1000Genomes East Asian Sub 1008 T=0.787 C=0.213
1000Genomes Europe Sub 1006 T=0.897 C=0.103
1000Genomes South Asian Sub 978 T=0.83 C=0.17
1000Genomes American Sub 694 T=0.87 C=0.13
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.859 C=0.141
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.896 C=0.104
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.899 C=0.101
Northern Sweden ACPOP Study-wide 600 T=0.89 C=0.12
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 T= A C Note
GRCh38.p12 chr 20 NC_000020.11:g.34...

NC_000020.11:g.34262569=

NC_000020.11:g.34...

NC_000020.11:g.34262569T>A

NC_000020.11:g.34...

NC_000020.11:g.34262569T>C

GRCh37.p13 chr 20 NC_000020.10:g.32...

NC_000020.10:g.32850375=

NC_000020.10:g.32...

NC_000020.10:g.32850375T>A

NC_000020.10:g.32...

NC_000020.10:g.32850375T>C

ASIP RefSeqGene NG_011439.1:g.7205= NG_011439.1:g.720...

NG_011439.1:g.7205T>A

NG_011439.1:g.720...

NG_011439.1:g.7205T>C

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#.

77 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3396422 Sep 28, 2001 (100)
2 YUSUKE ss5004774 Aug 28, 2002 (108)
3 SC_SNP ss8374617 Apr 21, 2003 (114)
4 ILLUMINA ss75118459 Dec 07, 2007 (129)
5 HGSV ss77461773 Dec 07, 2007 (129)
6 HGSV ss78945487 Dec 07, 2007 (129)
7 HGSV ss83518871 Dec 15, 2007 (130)
8 1000GENOMES ss113284588 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117532409 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119434737 Dec 01, 2009 (131)
11 GMI ss156386050 Dec 01, 2009 (131)
12 ILLUMINA ss160546685 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss169500375 Jul 04, 2010 (132)
14 ILLUMINA ss173340338 Jul 04, 2010 (132)
15 BUSHMAN ss203877237 Jul 04, 2010 (132)
16 1000GENOMES ss228333817 Jul 14, 2010 (132)
17 1000GENOMES ss237819072 Jul 15, 2010 (132)
18 1000GENOMES ss243992670 Jul 15, 2010 (132)
19 GMI ss283367956 May 04, 2012 (137)
20 PJP ss292644587 May 09, 2011 (134)
21 ILLUMINA ss480566222 May 04, 2012 (137)
22 ILLUMINA ss480580716 May 04, 2012 (137)
23 ILLUMINA ss481400996 Sep 08, 2015 (146)
24 ILLUMINA ss485078717 May 04, 2012 (137)
25 ILLUMINA ss537089831 Sep 08, 2015 (146)
26 TISHKOFF ss566224528 Apr 25, 2013 (138)
27 SSMP ss662107042 Apr 25, 2013 (138)
28 ILLUMINA ss780673528 Aug 21, 2014 (142)
29 ILLUMINA ss782985645 Sep 08, 2015 (146)
30 ILLUMINA ss783946572 Aug 21, 2014 (142)
31 ILLUMINA ss832242316 Sep 08, 2015 (146)
32 ILLUMINA ss836169699 Aug 21, 2014 (142)
33 EVA-GONL ss994683965 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1082178376 Aug 21, 2014 (142)
35 1000GENOMES ss1364626081 Aug 21, 2014 (142)
36 DDI ss1429045006 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1579493634 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1638702678 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1681696711 Apr 01, 2015 (144)
40 EVA_DECODE ss1698742662 Apr 01, 2015 (144)
41 EVA_SVP ss1713691093 Apr 01, 2015 (144)
42 ILLUMINA ss1752383576 Sep 08, 2015 (146)
43 HAMMER_LAB ss1809486111 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1938197462 Feb 12, 2016 (147)
45 JJLAB ss2029881041 Sep 14, 2016 (149)
46 USC_VALOUEV ss2158445111 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2242446778 Dec 20, 2016 (150)
48 TOPMED ss2408974850 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2629434299 Nov 08, 2017 (151)
50 ILLUMINA ss2633793453 Nov 08, 2017 (151)
51 GRF ss2704135052 Nov 08, 2017 (151)
52 GNOMAD ss2967003260 Nov 08, 2017 (151)
53 SWEGEN ss3018127073 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3028773493 Nov 08, 2017 (151)
55 CSHL ss3352496891 Nov 08, 2017 (151)
56 TOPMED ss3359485149 Nov 08, 2017 (151)
57 ILLUMINA ss3628382391 Oct 12, 2018 (152)
58 ILLUMINA ss3631750289 Oct 12, 2018 (152)
59 ILLUMINA ss3633249715 Oct 12, 2018 (152)
60 ILLUMINA ss3633963747 Oct 12, 2018 (152)
61 ILLUMINA ss3634833547 Oct 12, 2018 (152)
62 ILLUMINA ss3635648854 Oct 12, 2018 (152)
63 ILLUMINA ss3636525895 Oct 12, 2018 (152)
64 ILLUMINA ss3637400937 Oct 12, 2018 (152)
65 ILLUMINA ss3638343252 Oct 12, 2018 (152)
66 ILLUMINA ss3640540845 Oct 12, 2018 (152)
67 ILLUMINA ss3643306207 Oct 12, 2018 (152)
68 EGCUT_WGS ss3684806529 Jul 13, 2019 (153)
69 EVA_DECODE ss3706874748 Jul 13, 2019 (153)
70 ACPOP ss3743364880 Jul 13, 2019 (153)
71 ILLUMINA ss3745133444 Jul 13, 2019 (153)
72 EVA ss3758597552 Jul 13, 2019 (153)
73 ILLUMINA ss3772629663 Jul 13, 2019 (153)
74 PACBIO ss3788639005 Jul 13, 2019 (153)
75 PACBIO ss3793532814 Jul 13, 2019 (153)
76 PACBIO ss3798419708 Jul 13, 2019 (153)
77 KHV_HUMAN_GENOMES ss3821766376 Jul 13, 2019 (153)
78 1000Genomes NC_000020.10 - 32850375 Oct 12, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 32850375 Oct 12, 2018 (152)
80 Genetic variation in the Estonian population NC_000020.10 - 32850375 Oct 12, 2018 (152)
81 gnomAD - Genomes NC_000020.10 - 32850375 Jul 13, 2019 (153)
82 Northern Sweden NC_000020.10 - 32850375 Jul 13, 2019 (153)
83 TopMed NC_000020.11 - 34262569 Oct 12, 2018 (152)
84 UK 10K study - Twins NC_000020.10 - 32850375 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)
rs3818359 Oct 09, 2002 (108)
rs59385119 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss2242446778 NC_000020.11:34262568:T:A NC_000020.11:34262568:T:A (self)
ss77461773, ss78945487, ss83518871, ss113284588, ss117532409, ss169500375, ss203877237, ss283367956, ss292644587, ss480566222, ss1698742662, ss1713691093, ss3643306207 NC_000020.9:32314035:T:C NC_000020.11:34262568:T:C (self)
78084330, 43222683, 30544777, 213104618, 16649745, 43222683, ss228333817, ss237819072, ss243992670, ss480580716, ss481400996, ss485078717, ss537089831, ss566224528, ss662107042, ss780673528, ss782985645, ss783946572, ss832242316, ss836169699, ss994683965, ss1082178376, ss1364626081, ss1429045006, ss1579493634, ss1638702678, ss1681696711, ss1752383576, ss1809486111, ss1938197462, ss2029881041, ss2158445111, ss2408974850, ss2629434299, ss2633793453, ss2704135052, ss2967003260, ss3018127073, ss3352496891, ss3628382391, ss3631750289, ss3633249715, ss3633963747, ss3634833547, ss3635648854, ss3636525895, ss3637400937, ss3638343252, ss3640540845, ss3684806529, ss3743364880, ss3745133444, ss3758597552, ss3772629663, ss3788639005, ss3793532814, ss3798419708 NC_000020.10:32850374:T:C NC_000020.11:34262568:T:C (self)
226320539, ss2242446778, ss3028773493, ss3359485149, ss3706874748, ss3821766376 NC_000020.11:34262568:T:C NC_000020.11:34262568:T:C (self)
ss3396422, ss5004774, ss75118459, ss119434737, ss156386050, ss160546685, ss173340338 NT_011362.10:3046466:T:C NC_000020.11:34262568:T:C (self)
ss8374617 NT_028392.4:3017142:T:C NC_000020.11:34262568:T:C (self)
Help

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

1 citation for rs2424984
PMID Title Author Year Journal
20158590 Predicting phenotype from genotype: normal pigmentation. Valenzuela RK et al. 2010 Journal of forensic sciences

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