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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.

rs9881120

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:38144926 (GRCh38.p14) 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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.179640 (47549/264690, TOPMED)
T=0.180429 (23694/131320, GnomAD)
T=0.01568 (443/28248, 14KJPN) (+ 17 more)
T=0.15479 (2924/18890, ALFA)
T=0.01599 (268/16760, 8.3KJPN)
T=0.1563 (1001/6404, 1000G_30x)
T=0.1520 (761/5008, 1000G)
T=0.1308 (586/4480, Estonian)
T=0.1204 (464/3854, ALSPAC)
T=0.1168 (433/3708, TWINSUK)
T=0.0229 (67/2920, KOREAN)
T=0.2081 (392/1884, HapMap)
T=0.0147 (27/1832, Korea1K)
T=0.132 (79/600, NorthernSweden)
T=0.394 (85/216, Qatari)
A=0.405 (51/126, SGDP_PRJ)
T=0.21 (10/48, Ancient Sardinia)
T=0.07 (3/40, GENOME_DK)
A=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 A=0.84521 T=0.15479
European Sub 14286 A=0.87400 T=0.12600
African Sub 2946 A=0.6921 T=0.3079
African Others Sub 114 A=0.649 T=0.351
African American Sub 2832 A=0.6939 T=0.3061
Asian Sub 112 A=0.982 T=0.018
East Asian Sub 86 A=0.98 T=0.02
Other Asian Sub 26 A=1.00 T=0.00
Latin American 1 Sub 146 A=0.822 T=0.178
Latin American 2 Sub 610 A=0.908 T=0.092
South Asian Sub 98 A=0.95 T=0.05
Other Sub 692 A=0.815 T=0.185


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 A=0.820360 T=0.179640
gnomAD - Genomes Global Study-wide 131320 A=0.819571 T=0.180429
gnomAD - Genomes European Sub 71490 A=0.87583 T=0.12417
gnomAD - Genomes African Sub 39204 A=0.68656 T=0.31344
gnomAD - Genomes American Sub 12268 A=0.87097 T=0.12903
gnomAD - Genomes Ashkenazi Jewish Sub 3282 A=0.8394 T=0.1606
gnomAD - Genomes East Asian Sub 3072 A=0.9723 T=0.0277
gnomAD - Genomes Other Sub 2004 A=0.8333 T=0.1667
14KJPN JAPANESE Study-wide 28248 A=0.98432 T=0.01568
Allele Frequency Aggregator Total Global 18890 A=0.84521 T=0.15479
Allele Frequency Aggregator European Sub 14286 A=0.87400 T=0.12600
Allele Frequency Aggregator African Sub 2946 A=0.6921 T=0.3079
Allele Frequency Aggregator Other Sub 692 A=0.815 T=0.185
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.908 T=0.092
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.822 T=0.178
Allele Frequency Aggregator Asian Sub 112 A=0.982 T=0.018
Allele Frequency Aggregator South Asian Sub 98 A=0.95 T=0.05
8.3KJPN JAPANESE Study-wide 16760 A=0.98401 T=0.01599
1000Genomes_30x Global Study-wide 6404 A=0.8437 T=0.1563
1000Genomes_30x African Sub 1786 A=0.6422 T=0.3578
1000Genomes_30x Europe Sub 1266 A=0.8697 T=0.1303
1000Genomes_30x South Asian Sub 1202 A=0.9384 T=0.0616
1000Genomes_30x East Asian Sub 1170 A=0.9778 T=0.0222
1000Genomes_30x American Sub 980 A=0.901 T=0.099
1000Genomes Global Study-wide 5008 A=0.8480 T=0.1520
1000Genomes African Sub 1322 A=0.6407 T=0.3593
1000Genomes East Asian Sub 1008 A=0.9752 T=0.0248
1000Genomes Europe Sub 1006 A=0.8678 T=0.1322
1000Genomes South Asian Sub 978 A=0.937 T=0.063
1000Genomes American Sub 694 A=0.905 T=0.095
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8692 T=0.1308
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8796 T=0.1204
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8832 T=0.1168
KOREAN population from KRGDB KOREAN Study-wide 2920 A=0.9771 T=0.0229
HapMap Global Study-wide 1884 A=0.7919 T=0.2081
HapMap American Sub 764 A=0.897 T=0.103
HapMap African Sub 690 A=0.600 T=0.400
HapMap Asian Sub 254 A=0.980 T=0.020
HapMap Europe Sub 176 A=0.818 T=0.182
Korean Genome Project KOREAN Study-wide 1832 A=0.9853 T=0.0147
Northern Sweden ACPOP Study-wide 600 A=0.868 T=0.132
Qatari Global Study-wide 216 A=0.606 T=0.394
SGDP_PRJ Global Study-wide 126 A=0.405 T=0.595
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 48 A=0.79 T=0.21
The Danish reference pan genome Danish Study-wide 40 A=0.93 T=0.07
Siberian Global Study-wide 10 A=0.5 T=0.5
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.p14 chr 3 NC_000003.12:g.38144926A>T
GRCh37.p13 chr 3 NC_000003.11:g.38186417A>T
MYD88 RefSeqGene (LRG_157) NG_016964.1:g.11449A>T
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

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 A= T
GRCh38.p14 chr 3 NC_000003.12:g.38144926= NC_000003.12:g.38144926A>T
GRCh37.p13 chr 3 NC_000003.11:g.38186417= NC_000003.11:g.38186417A>T
MYD88 RefSeqGene (LRG_157) NG_016964.1:g.11449= NG_016964.1:g.11449A>T
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#.

58 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss13716906 Dec 05, 2003 (119)
2 WUGSC_SSAHASNP ss13828857 Dec 05, 2003 (126)
3 BCM_SSAHASNP ss22987857 Apr 05, 2004 (126)
4 WUGSC_SSAHASNP ss23043722 Apr 05, 2004 (126)
5 AFFY ss66501333 Nov 29, 2006 (127)
6 AFFY ss76324139 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82624075 Dec 15, 2007 (130)
8 SNP500CANCER ss105440340 Feb 06, 2009 (130)
9 ILLUMINA-UK ss117051808 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss162051377 Jul 04, 2010 (132)
11 AFFY ss173262815 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss206184816 Jul 04, 2010 (132)
13 1000GENOMES ss220090359 Jul 14, 2010 (132)
14 1000GENOMES ss231787546 Jul 14, 2010 (132)
15 TISHKOFF ss556554532 Apr 25, 2013 (138)
16 SSMP ss650228790 Apr 25, 2013 (138)
17 EVA-GONL ss978488399 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1070336423 Aug 21, 2014 (142)
19 1000GENOMES ss1303598599 Aug 21, 2014 (142)
20 DDI ss1429391498 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1579926882 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1606849870 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1649843903 Apr 01, 2015 (144)
24 EVA_SVP ss1712568531 Apr 01, 2015 (144)
25 HAMMER_LAB ss1799154815 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1921733123 Feb 12, 2016 (147)
27 USC_VALOUEV ss2149495034 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2250718759 Dec 20, 2016 (150)
29 GNOMAD ss2791779853 Nov 08, 2017 (151)
30 SWEGEN ss2992149380 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3024475582 Nov 08, 2017 (151)
32 CSHL ss3344977357 Nov 08, 2017 (151)
33 EGCUT_WGS ss3660066824 Jul 13, 2019 (153)
34 EVA_DECODE ss3709033045 Jul 13, 2019 (153)
35 ACPOP ss3729805058 Jul 13, 2019 (153)
36 EVA ss3759908391 Jul 13, 2019 (153)
37 PACBIO ss3784286594 Jul 13, 2019 (153)
38 PACBIO ss3789807454 Jul 13, 2019 (153)
39 PACBIO ss3794681264 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3803055176 Jul 13, 2019 (153)
41 EVA ss3827762114 Apr 25, 2020 (154)
42 SGDP_PRJ ss3855642897 Apr 25, 2020 (154)
43 KRGDB ss3901454762 Apr 25, 2020 (154)
44 KOGIC ss3951045015 Apr 25, 2020 (154)
45 EVA ss3984985294 Apr 26, 2021 (155)
46 TOPMED ss4561087247 Apr 26, 2021 (155)
47 TOMMO_GENOMICS ss5158687766 Apr 26, 2021 (155)
48 1000G_HIGH_COVERAGE ss5253737551 Oct 13, 2022 (156)
49 EVA ss5339158356 Oct 13, 2022 (156)
50 EVA ss5506958192 Oct 13, 2022 (156)
51 1000G_HIGH_COVERAGE ss5531924249 Oct 13, 2022 (156)
52 SANFORD_IMAGENETICS ss5631941970 Oct 13, 2022 (156)
53 TOMMO_GENOMICS ss5690204044 Oct 13, 2022 (156)
54 YY_MCH ss5803654859 Oct 13, 2022 (156)
55 EVA ss5825618093 Oct 13, 2022 (156)
56 EVA ss5853574333 Oct 13, 2022 (156)
57 EVA ss5868428698 Oct 13, 2022 (156)
58 EVA ss5960222138 Oct 13, 2022 (156)
59 1000Genomes NC_000003.11 - 38186417 Oct 12, 2018 (152)
60 1000Genomes_30x NC_000003.12 - 38144926 Oct 13, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 38186417 Oct 12, 2018 (152)
62 Genetic variation in the Estonian population NC_000003.11 - 38186417 Oct 12, 2018 (152)
63 The Danish reference pan genome NC_000003.11 - 38186417 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000003.12 - 38144926 Apr 26, 2021 (155)
65 HapMap NC_000003.12 - 38144926 Apr 25, 2020 (154)
66 KOREAN population from KRGDB NC_000003.11 - 38186417 Apr 25, 2020 (154)
67 Korean Genome Project NC_000003.12 - 38144926 Apr 25, 2020 (154)
68 Northern Sweden NC_000003.11 - 38186417 Jul 13, 2019 (153)
69 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000003.11 - 38186417 Apr 26, 2021 (155)
70 Qatari NC_000003.11 - 38186417 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000003.11 - 38186417 Apr 25, 2020 (154)
72 Siberian NC_000003.11 - 38186417 Apr 25, 2020 (154)
73 8.3KJPN NC_000003.11 - 38186417 Apr 26, 2021 (155)
74 14KJPN NC_000003.12 - 38144926 Oct 13, 2022 (156)
75 TopMed NC_000003.12 - 38144926 Apr 26, 2021 (155)
76 UK 10K study - Twins NC_000003.11 - 38186417 Oct 12, 2018 (152)
77 ALFA NC_000003.12 - 38144926 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)
rs9985497 Mar 10, 2006 (126)
rs12715309 Mar 10, 2006 (126)
rs59860838 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66501333, ss76324139, ss117051808, ss162051377, ss173262815, ss206184816, ss1712568531 NC_000003.10:38161420:A:T NC_000003.12:38144925:A:T (self)
14772462, 8208301, 5805072, 6091821, 8632156, 3089923, 211221, 3775053, 7659877, 2011388, 16657073, 8208301, ss220090359, ss231787546, ss556554532, ss650228790, ss978488399, ss1070336423, ss1303598599, ss1429391498, ss1579926882, ss1606849870, ss1649843903, ss1799154815, ss1921733123, ss2149495034, ss2791779853, ss2992149380, ss3344977357, ss3660066824, ss3729805058, ss3759908391, ss3784286594, ss3789807454, ss3794681264, ss3827762114, ss3855642897, ss3901454762, ss3984985294, ss5158687766, ss5339158356, ss5506958192, ss5631941970, ss5825618093, ss5960222138 NC_000003.11:38186416:A:T NC_000003.12:38144925:A:T (self)
19450184, 104780554, 2342036, 7423016, 24041148, 398464802, 2156723688, ss2250718759, ss3024475582, ss3709033045, ss3803055176, ss3951045015, ss4561087247, ss5253737551, ss5531924249, ss5690204044, ss5803654859, ss5853574333, ss5868428698 NC_000003.12:38144925:A:T NC_000003.12:38144925:A:T (self)
ss13716906, ss13828857, ss22987857 NT_022517.16:38112041:A:T NC_000003.12:38144925:A:T (self)
ss23043722, ss82624075, ss105440340 NT_022517.18:38126416:A:T NC_000003.12:38144925:A:T (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 rs9881120

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.post761+d5e8e07