Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs4775889

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:50484443 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.152752 (40432/264690, TOPMED)
G=0.137563 (19286/140198, GnomAD)
G=0.13992 (3407/24350, ALFA) (+ 15 more)
G=0.1209 (774/6404, 1000G_30x)
G=0.1212 (607/5008, 1000G)
G=0.0804 (360/4480, Estonian)
G=0.1609 (620/3854, ALSPAC)
G=0.1726 (640/3708, TWINSUK)
G=0.0000 (0/2922, KOREAN)
G=0.1159 (200/1726, HapMap)
G=0.155 (155/998, GoNL)
G=0.152 (91/600, NorthernSweden)
G=0.043 (23/534, MGP)
G=0.278 (60/216, Qatari)
A=0.417 (50/120, SGDP_PRJ)
G=0.15 (6/40, GENOME_DK)
A=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
USP8 : Intron Variant
Publications
1 citation
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 24350 A=0.86008 G=0.13992 0.744723 0.024559 0.230719 12
European Sub 18126 A=0.84839 G=0.15161 0.72316 0.026371 0.250469 4
African Sub 4114 A=0.9409 G=0.0591 0.888187 0.00632 0.105493 3
African Others Sub 148 A=0.939 G=0.061 0.878378 0.0 0.121622 0
African American Sub 3966 A=0.9410 G=0.0590 0.888553 0.006556 0.104892 4
Asian Sub 124 A=0.992 G=0.008 0.983871 0.0 0.016129 0
East Asian Sub 96 A=0.99 G=0.01 0.979167 0.0 0.020833 0
Other Asian Sub 28 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 168 A=0.798 G=0.202 0.642857 0.047619 0.309524 0
Latin American 2 Sub 670 A=0.703 G=0.297 0.498507 0.092537 0.408955 0
South Asian Sub 98 A=0.84 G=0.16 0.714286 0.040816 0.244898 0
Other Sub 1050 A=0.8419 G=0.1581 0.702857 0.019048 0.278095 1


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=0.847248 G=0.152752
gnomAD - Genomes Global Study-wide 140198 A=0.862437 G=0.137563
gnomAD - Genomes European Sub 75934 A=0.84737 G=0.15263
gnomAD - Genomes African Sub 42014 A=0.93626 G=0.06374
gnomAD - Genomes American Sub 13646 A=0.72673 G=0.27327
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.7231 G=0.2769
gnomAD - Genomes East Asian Sub 3132 A=0.9965 G=0.0035
gnomAD - Genomes Other Sub 2150 A=0.8335 G=0.1665
Allele Frequency Aggregator Total Global 24350 A=0.86008 G=0.13992
Allele Frequency Aggregator European Sub 18126 A=0.84839 G=0.15161
Allele Frequency Aggregator African Sub 4114 A=0.9409 G=0.0591
Allele Frequency Aggregator Other Sub 1050 A=0.8419 G=0.1581
Allele Frequency Aggregator Latin American 2 Sub 670 A=0.703 G=0.297
Allele Frequency Aggregator Latin American 1 Sub 168 A=0.798 G=0.202
Allele Frequency Aggregator Asian Sub 124 A=0.992 G=0.008
Allele Frequency Aggregator South Asian Sub 98 A=0.84 G=0.16
1000Genomes_30x Global Study-wide 6404 A=0.8791 G=0.1209
1000Genomes_30x African Sub 1786 A=0.9675 G=0.0325
1000Genomes_30x Europe Sub 1266 A=0.8191 G=0.1809
1000Genomes_30x South Asian Sub 1202 A=0.8020 G=0.1980
1000Genomes_30x East Asian Sub 1170 A=0.9983 G=0.0017
1000Genomes_30x American Sub 980 A=0.748 G=0.252
1000Genomes Global Study-wide 5008 A=0.8788 G=0.1212
1000Genomes African Sub 1322 A=0.9607 G=0.0393
1000Genomes East Asian Sub 1008 A=0.9980 G=0.0020
1000Genomes Europe Sub 1006 A=0.8171 G=0.1829
1000Genomes South Asian Sub 978 A=0.800 G=0.200
1000Genomes American Sub 694 A=0.751 G=0.249
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9196 G=0.0804
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8391 G=0.1609
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8274 G=0.1726
KOREAN population from KRGDB KOREAN Study-wide 2922 A=1.0000 G=0.0000
HapMap Global Study-wide 1726 A=0.8841 G=0.1159
HapMap American Sub 770 A=0.858 G=0.142
HapMap African Sub 692 A=0.929 G=0.071
HapMap Europe Sub 176 A=0.761 G=0.239
HapMap Asian Sub 88 A=1.00 G=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.845 G=0.155
Northern Sweden ACPOP Study-wide 600 A=0.848 G=0.152
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.957 G=0.043
Qatari Global Study-wide 216 A=0.722 G=0.278
SGDP_PRJ Global Study-wide 120 A=0.417 G=0.583
The Danish reference pan genome Danish Study-wide 40 A=0.85 G=0.15
Siberian Global Study-wide 8 A=0.5 G=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 15 NC_000015.10:g.50484443A>G
GRCh37.p13 chr 15 NC_000015.9:g.50776640A>G
USP8 RefSeqGene NG_047101.1:g.65067A>G
Gene: USP8, ubiquitin specific peptidase 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
USP8 transcript variant 2 NM_001128610.3:c.1890+82A…

NM_001128610.3:c.1890+82A>G

 		N/A Intron Variant
USP8 transcript variant 4 NM_001283049.2:c.1572+237…

NM_001283049.2:c.1572+2378A>G

 		N/A Intron Variant
USP8 transcript variant 1 NM_005154.5:c.1890+82A>G N/A Intron 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

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= G
GRCh38.p14 chr 15 NC_000015.10:g.50484443= NC_000015.10:g.50484443A>G
GRCh37.p13 chr 15 NC_000015.9:g.50776640= NC_000015.9:g.50776640A>G
USP8 RefSeqGene NG_047101.1:g.65067= NG_047101.1:g.65067A>G
USP8 transcript variant 2 NM_001128610.1:c.1890+82= NM_001128610.1:c.1890+82A>G
USP8 transcript variant 2 NM_001128610.3:c.1890+82= NM_001128610.3:c.1890+82A>G
USP8 transcript variant 3 NM_001128611.1:c.1890+82= NM_001128611.1:c.1890+82A>G
USP8 transcript variant 4 NM_001283049.2:c.1572+2378= NM_001283049.2:c.1572+2378A>G
USP8 transcript variant 1 NM_005154.3:c.1890+82= NM_005154.3:c.1890+82A>G
USP8 transcript variant 1 NM_005154.5:c.1890+82= NM_005154.5:c.1890+82A>G
USP8 transcript variant X1 XM_005254775.1:c.1803+2378= XM_005254775.1:c.1803+2378A>G
USP8 transcript variant X2 XM_005254776.1:c.1572+2378= XM_005254776.1:c.1572+2378A>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#.

68 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6589198 Feb 20, 2003 (111)
2 WI_SSAHASNP ss12325956 Jul 11, 2003 (116)
3 PERLEGEN ss24665694 Sep 20, 2004 (123)
4 ILLUMINA ss75121404 Dec 07, 2007 (129)
5 BCMHGSC_JDW ss90151249 Mar 24, 2008 (129)
6 KRIBB_YJKIM ss119487877 Dec 01, 2009 (131)
7 ENSEMBL ss136336415 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss167977780 Jul 04, 2010 (132)
9 ILLUMINA ss173807991 Jul 04, 2010 (132)
10 BUSHMAN ss200828017 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss207219619 Jul 04, 2010 (132)
12 1000GENOMES ss236773702 Jul 15, 2010 (132)
13 BL ss254971348 May 09, 2011 (134)
14 ILLUMINA ss410936006 Sep 17, 2011 (135)
15 ILLUMINA ss537272414 Sep 08, 2015 (146)
16 TISHKOFF ss564474300 Apr 25, 2013 (138)
17 SSMP ss660196063 Apr 25, 2013 (138)
18 EVA-GONL ss991774645 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1080115993 Aug 21, 2014 (142)
20 1000GENOMES ss1353419870 Aug 21, 2014 (142)
21 DDI ss1427622097 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1577607618 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1632973218 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1675967251 Apr 01, 2015 (144)
25 EVA_DECODE ss1695791709 Apr 01, 2015 (144)
26 EVA_MGP ss1711397368 Apr 01, 2015 (144)
27 EVA_SVP ss1713488914 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1935178024 Feb 12, 2016 (147)
29 GENOMED ss1968103603 Jul 19, 2016 (147)
30 JJLAB ss2028368516 Sep 14, 2016 (149)
31 USC_VALOUEV ss2156770048 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2206685208 Dec 20, 2016 (150)
33 ILLUMINA ss2633227299 Nov 08, 2017 (151)
34 GNOMAD ss2934781383 Nov 08, 2017 (151)
35 SWEGEN ss3013264280 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3028007434 Nov 08, 2017 (151)
37 CSHL ss3351109948 Nov 08, 2017 (151)
38 ILLUMINA ss3627358232 Oct 12, 2018 (152)
39 ILLUMINA ss3638084906 Oct 12, 2018 (152)
40 ILLUMINA ss3643069169 Oct 12, 2018 (152)
41 OMUKHERJEE_ADBS ss3646474431 Oct 12, 2018 (152)
42 EGCUT_WGS ss3680405933 Jul 13, 2019 (153)
43 EVA_DECODE ss3697870101 Jul 13, 2019 (153)
44 ACPOP ss3740913321 Jul 13, 2019 (153)
45 EVA ss3753070636 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3818388466 Jul 13, 2019 (153)
47 EVA ss3825858990 Apr 27, 2020 (154)
48 EVA ss3834228455 Apr 27, 2020 (154)
49 SGDP_PRJ ss3882893868 Apr 27, 2020 (154)
50 KRGDB ss3932056391 Apr 27, 2020 (154)
51 FSA-LAB ss3984073143 Apr 27, 2021 (155)
52 EVA ss3986648315 Apr 27, 2021 (155)
53 EVA ss4017701173 Apr 27, 2021 (155)
54 TOPMED ss4991008836 Apr 27, 2021 (155)
55 1000G_HIGH_COVERAGE ss5298402975 Oct 16, 2022 (156)
56 HUGCELL_USP ss5492135464 Oct 16, 2022 (156)
57 1000G_HIGH_COVERAGE ss5599789219 Oct 16, 2022 (156)
58 EVA ss5623964341 Oct 16, 2022 (156)
59 EVA ss5624052970 Oct 16, 2022 (156)
60 SANFORD_IMAGENETICS ss5657487720 Oct 16, 2022 (156)
61 EVA ss5800193366 Oct 16, 2022 (156)
62 YY_MCH ss5815323046 Oct 16, 2022 (156)
63 EVA ss5828186637 Oct 16, 2022 (156)
64 EVA ss5848402045 Oct 16, 2022 (156)
65 EVA ss5875832236 Oct 16, 2022 (156)
66 EVA ss5936560301 Oct 16, 2022 (156)
67 EVA ss5948887443 Oct 16, 2022 (156)
68 EVA ss5980868318 Oct 16, 2022 (156)
69 1000Genomes NC_000015.9 - 50776640 Oct 12, 2018 (152)
70 1000Genomes_30x NC_000015.10 - 50484443 Oct 16, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 50776640 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000015.9 - 50776640 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000015.9 - 50776640 Apr 27, 2020 (154)
74 gnomAD - Genomes NC_000015.10 - 50484443 Apr 27, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000015.9 - 50776640 Apr 27, 2020 (154)
76 HapMap NC_000015.10 - 50484443 Apr 27, 2020 (154)
77 KOREAN population from KRGDB NC_000015.9 - 50776640 Apr 27, 2020 (154)
78 Medical Genome Project healthy controls from Spanish population NC_000015.9 - 50776640 Apr 27, 2020 (154)
79 Northern Sweden NC_000015.9 - 50776640 Jul 13, 2019 (153)
80 Qatari NC_000015.9 - 50776640 Apr 27, 2020 (154)
81 SGDP_PRJ NC_000015.9 - 50776640 Apr 27, 2020 (154)
82 Siberian NC_000015.9 - 50776640 Apr 27, 2020 (154)
83 TopMed NC_000015.10 - 50484443 Apr 27, 2021 (155)
84 UK 10K study - Twins NC_000015.9 - 50776640 Oct 12, 2018 (152)
85 ALFA NC_000015.10 - 50484443 Apr 27, 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)
rs17597943 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90151249, ss167977780, ss200828017, ss207219619, ss254971348, ss1695791709, ss1713488914, ss3643069169 NC_000015.8:48563931:A:G NC_000015.10:50484442:A:G (self)
66490318, 36909392, 26144181, 3851452, 16483386, 39233785, 513128, 14198186, 17219954, 34910848, 9286402, 36909392, ss236773702, ss537272414, ss564474300, ss660196063, ss991774645, ss1080115993, ss1353419870, ss1427622097, ss1577607618, ss1632973218, ss1675967251, ss1711397368, ss1935178024, ss1968103603, ss2028368516, ss2156770048, ss2633227299, ss2934781383, ss3013264280, ss3351109948, ss3627358232, ss3638084906, ss3646474431, ss3680405933, ss3740913321, ss3753070636, ss3825858990, ss3834228455, ss3882893868, ss3932056391, ss3984073143, ss3986648315, ss4017701173, ss5623964341, ss5624052970, ss5657487720, ss5800193366, ss5828186637, ss5848402045, ss5936560301, ss5948887443, ss5980868318 NC_000015.9:50776639:A:G NC_000015.10:50484442:A:G (self)
87315154, 468755882, 1261051, 206554496, 5397222779, ss2206685208, ss3028007434, ss3697870101, ss3818388466, ss4991008836, ss5298402975, ss5492135464, ss5599789219, ss5815323046, ss5875832236 NC_000015.10:50484442:A:G NC_000015.10:50484442:A:G (self)
ss12325956 NT_010194.15:21566250:A:G NC_000015.10:50484442:A:G (self)
ss6589198, ss24665694, ss75121404, ss119487877, ss136336415, ss173807991, ss410936006 NT_010194.17:21567196:A:G NC_000015.10:50484442:A:G (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 rs4775889
PMID Title Author Year Journal
20011102 Fine-scale variation and genetic determinants of alternative splicing across individuals. Coulombe-Huntington J et al. 2009 PLoS genetics
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.post820+afb47a3d