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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs1984905

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:80462 (GRCh38.p13) 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>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.227950 (60336/264690, TOPMED)
T=0.208933 (29274/140112, GnomAD)
T=0.18497 (4594/24836, ALFA) (+ 11 more)
C=0.38144 (6393/16760, 8.3KJPN)
T=0.3169 (1587/5008, 1000G)
T=0.1707 (658/3854, ALSPAC)
T=0.1807 (670/3708, TWINSUK)
C=0.4222 (1237/2930, KOREAN)
T=0.152 (152/998, GoNL)
T=0.193 (116/600, NorthernSweden)
T=0.150 (80/534, MGP)
T=0.221 (104/470, SGDP_PRJ)
T=0.139 (30/216, Qatari)
T=0.25 (12/48, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 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.p13 chr 10 NC_000010.11:g.80462T>C
GRCh38.p13 chr 10 NC_000010.11:g.80462T>G
GRCh37.p13 chr 10 NC_000010.10:g.126402T>C
GRCh37.p13 chr 10 NC_000010.10:g.126402T>G
IL9RP2 pseudogene NG_009864.2:g.5884A>G
IL9RP2 pseudogene NG_009864.2:g.5884A>C
TUBB8 RefSeqGene NG_046777.1:g.994A>G
TUBB8 RefSeqGene NG_046777.1:g.994A>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.70462T>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.70462T>G
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

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 24836 T=0.18497 C=0.81503
European Sub 19978 T=0.16553 C=0.83447
African Sub 3024 T=0.2450 C=0.7550
African Others Sub 118 T=0.322 C=0.678
African American Sub 2906 T=0.2419 C=0.7581
Asian Sub 120 T=0.492 C=0.508
East Asian Sub 94 T=0.49 C=0.51
Other Asian Sub 26 T=0.50 C=0.50
Latin American 1 Sub 148 T=0.142 C=0.858
Latin American 2 Sub 622 T=0.400 C=0.600
South Asian Sub 98 T=0.33 C=0.67
Other Sub 846 T=0.219 C=0.781


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 264690 T=0.227950 C=0.772050
gnomAD - Genomes Global Study-wide 140112 T=0.208933 C=0.791067
gnomAD - Genomes European Sub 75882 T=0.16801 C=0.83199
gnomAD - Genomes African Sub 41986 T=0.24227 C=0.75773
gnomAD - Genomes American Sub 13648 T=0.27623 C=0.72377
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.1629 C=0.8371
gnomAD - Genomes East Asian Sub 3124 T=0.5138 C=0.4862
gnomAD - Genomes Other Sub 2150 T=0.2033 C=0.7967
8.3KJPN JAPANESE Study-wide 16760 T=0.61856 C=0.38144
1000Genomes Global Study-wide 5008 T=0.3169 C=0.6831
1000Genomes African Sub 1322 T=0.2428 C=0.7572
1000Genomes East Asian Sub 1008 T=0.5456 C=0.4544
1000Genomes Europe Sub 1006 T=0.1561 C=0.8439
1000Genomes South Asian Sub 978 T=0.357 C=0.643
1000Genomes American Sub 694 T=0.303 C=0.697
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1707 C=0.8293
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1807 C=0.8193
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5778 C=0.4222, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.152 C=0.848
Northern Sweden ACPOP Study-wide 600 T=0.193 C=0.807
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.150 C=0.850
SGDP_PRJ Global Study-wide 470 T=0.221 C=0.779
Qatari Global Study-wide 216 T=0.139 C=0.861
Siberian Global Study-wide 48 T=0.25 C=0.75
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= C G
GRCh38.p13 chr 10 NC_000010.11:g.80462= NC_000010.11:g.80462T>C NC_000010.11:g.80462T>G
GRCh37.p13 chr 10 NC_000010.10:g.126402= NC_000010.10:g.126402T>C NC_000010.10:g.126402T>G
IL9RP2 pseudogene NG_009864.2:g.5884= NG_009864.2:g.5884A>G NG_009864.2:g.5884A>C
TUBB8 RefSeqGene NG_046777.1:g.994= NG_046777.1:g.994A>G NG_046777.1:g.994A>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.70462= NW_003571043.1:g.70462T>C NW_003571043.1:g.70462T>G
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, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2892045 Jan 12, 2001 (92)
2 SC_JCM ss5805290 Feb 20, 2003 (124)
3 SC_SNP ss12973421 Dec 05, 2003 (124)
4 SC_SNP ss16089674 Feb 27, 2004 (124)
5 SSAHASNP ss20617039 Apr 05, 2004 (124)
6 PERLEGEN ss23881166 Sep 20, 2004 (124)
7 HGSV ss77206598 Dec 06, 2007 (129)
8 BCMHGSC_JDW ss88057399 Mar 23, 2008 (129)
9 BGI ss102844552 Dec 01, 2009 (131)
10 ENSEMBL ss107935983 Feb 03, 2009 (130)
11 1000GENOMES ss109145724 Jan 23, 2009 (130)
12 1000GENOMES ss115221456 Jan 25, 2009 (130)
13 ILLUMINA-UK ss118963223 Feb 15, 2009 (130)
14 ENSEMBL ss138806766 Dec 01, 2009 (131)
15 GMI ss158077323 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss167614003 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss168823574 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss170209990 Jul 04, 2010 (132)
19 BUSHMAN ss201023274 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss207204218 Jul 04, 2010 (132)
21 1000GENOMES ss224512339 Jul 14, 2010 (132)
22 1000GENOMES ss235012235 Jul 15, 2010 (132)
23 1000GENOMES ss241753208 Jul 15, 2010 (132)
24 BL ss253971509 May 09, 2011 (134)
25 GMI ss280440369 May 04, 2012 (137)
26 PJP ss290815784 May 09, 2011 (134)
27 ILLUMINA ss480026339 May 04, 2012 (137)
28 ILLUMINA ss482478368 May 04, 2012 (137)
29 TISHKOFF ss561707908 Apr 25, 2013 (138)
30 SSMP ss656208237 Apr 25, 2013 (138)
31 ILLUMINA ss779696664 Aug 21, 2014 (142)
32 ILLUMINA ss781128318 Aug 21, 2014 (142)
33 ILLUMINA ss835170695 Aug 21, 2014 (142)
34 EVA-GONL ss987096716 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1076687377 Aug 21, 2014 (142)
36 1000GENOMES ss1335912663 Aug 21, 2014 (142)
37 DDI ss1426189092 Apr 09, 2015 (144)
38 EVA_DECODE ss1596744214 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1623797505 Apr 09, 2015 (144)
40 EVA_UK10K_TWINSUK ss1666791538 Apr 09, 2015 (144)
41 EVA_MGP ss1711245162 Apr 09, 2015 (144)
42 HAMMER_LAB ss1806212535 Sep 11, 2015 (146)
43 WEILL_CORNELL_DGM ss1930414700 Feb 17, 2016 (147)
44 JJLAB ss2025929539 Sep 28, 2016 (149)
45 USC_VALOUEV ss2154169595 Oct 12, 2018 (152)
46 TOPMED ss2334634855 Oct 12, 2018 (152)
47 SYSTEMSBIOZJU ss2627432614 Oct 12, 2018 (152)
48 ILLUMINA ss2632661386 Oct 12, 2018 (152)
49 GRF ss2698388990 Oct 12, 2018 (152)
50 GNOMAD ss2884518457 Oct 12, 2018 (152)
51 SWEGEN ss3005784280 Oct 12, 2018 (152)
52 BIOINF_KMB_FNS_UNIBA ss3026746697 Nov 08, 2017 (151)
53 TOPMED ss3109330830 Nov 08, 2017 (151)
54 CSHL ss3348911580 Oct 12, 2018 (152)
55 ILLUMINA ss3630689698 Oct 12, 2018 (152)
56 ILLUMINA ss3641655086 Oct 12, 2018 (152)
57 OMUKHERJEE_ADBS ss3646401705 Oct 12, 2018 (152)
58 URBANLAB ss3649265484 Oct 12, 2018 (152)
59 EVA_DECODE ss3689095245 Jul 13, 2019 (153)
60 ACPOP ss3736974261 Jul 13, 2019 (153)
61 EVA ss3747627279 Jul 13, 2019 (153)
62 PACBIO ss3786553484 Jul 13, 2019 (153)
63 PACBIO ss3791748140 Jul 13, 2019 (153)
64 PACBIO ss3796629762 Jul 13, 2019 (153)
65 KHV_HUMAN_GENOMES ss3812993264 Jul 13, 2019 (153)
66 EVA ss3831916715 Apr 26, 2020 (154)
67 EVA ss3839487143 Apr 26, 2020 (154)
68 EVA ss3844952611 Apr 26, 2020 (154)
69 SGDP_PRJ ss3873326329 Apr 26, 2020 (154)
70 KRGDB ss3921253303 Apr 26, 2020 (154)
71 GNOMAD ss4211409081 Apr 26, 2021 (155)
72 TOPMED ss4839522069 Apr 26, 2021 (155)
73 TOMMO_GENOMICS ss5195847832 Apr 26, 2021 (155)
74 1000Genomes NC_000010.10 - 126402 Oct 12, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 126402 Oct 12, 2018 (152)
76 gnomAD - Genomes NC_000010.11 - 80462 Apr 26, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000010.10 - 126402 Apr 26, 2020 (154)
78 KOREAN population from KRGDB NC_000010.10 - 126402 Apr 26, 2020 (154)
79 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 126402 Apr 26, 2020 (154)
80 Northern Sweden NC_000010.10 - 126402 Jul 13, 2019 (153)
81 Qatari NC_000010.10 - 126402 Apr 26, 2020 (154)
82 SGDP_PRJ NC_000010.10 - 126402 Apr 26, 2020 (154)
83 Siberian NC_000010.10 - 126402 Apr 26, 2020 (154)
84 8.3KJPN NC_000010.10 - 126402 Apr 26, 2021 (155)
85 TopMed NC_000010.11 - 80462 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000010.10 - 126402 Oct 12, 2018 (152)
87 ALFA NC_000010.11 - 80462 Apr 26, 2021 (155)
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)
rs4359129 Dec 02, 2004 (124)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77206598 NC_000010.8:116401:T:C NC_000010.11:80461:T:C (self)
ss88057399, ss109145724, ss115221456, ss118963223, ss167614003, ss168823574, ss170209990, ss201023274, ss207204218, ss253971509, ss280440369, ss290815784, ss482478368, ss1596744214 NC_000010.9:116401:T:C NC_000010.11:80461:T:C (self)
48246360, 26806275, 11953843, 28430697, 360922, 10259126, 12456630, 25343309, 6685949, 53817139, 26806275, ss224512339, ss235012235, ss241753208, ss480026339, ss561707908, ss656208237, ss779696664, ss781128318, ss835170695, ss987096716, ss1076687377, ss1335912663, ss1426189092, ss1623797505, ss1666791538, ss1711245162, ss1806212535, ss1930414700, ss2025929539, ss2154169595, ss2334634855, ss2627432614, ss2632661386, ss2698388990, ss2884518457, ss3005784280, ss3348911580, ss3630689698, ss3641655086, ss3646401705, ss3736974261, ss3747627279, ss3786553484, ss3791748140, ss3796629762, ss3831916715, ss3839487143, ss3873326329, ss3921253303, ss5195847832 NC_000010.10:126401:T:C NC_000010.11:80461:T:C (self)
340932259, 34601362, 55067724, 4666836180, ss3026746697, ss3109330830, ss3649265484, ss3689095245, ss3812993264, ss3844952611, ss4211409081, ss4839522069 NC_000010.11:80461:T:C NC_000010.11:80461:T:C (self)
ss2892045, ss5805290, ss23881166, ss102844552, ss107935983, ss138806766, ss158077323 NT_008705.16:66401:T:C NC_000010.11:80461:T:C (self)
ss12973421 NT_024115.14:66401:T:C NC_000010.11:80461:T:C (self)
ss16089674, ss20617039 NT_077567.3:66401:T:C NC_000010.11:80461:T:C (self)
28430697, ss3921253303 NC_000010.10:126401:T:G NC_000010.11:80461:T:G (self)
Help

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

No publications for rs1984905

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad