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.

rs3752802

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:3144115 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.222785 (58969/264690, TOPMED)
A=0.223422 (31297/140080, GnomAD)
A=0.22171 (6265/28258, 14KJPN) (+ 18 more)
A=0.23785 (4493/18890, ALFA)
A=0.22554 (3780/16760, 8.3KJPN)
A=0.1968 (1260/6404, 1000G_30x)
A=0.2005 (1004/5008, 1000G)
A=0.2288 (1025/4480, Estonian)
A=0.2903 (1119/3854, ALSPAC)
A=0.2810 (1042/3708, TWINSUK)
A=0.2290 (671/2930, KOREAN)
A=0.2331 (427/1832, Korea1K)
A=0.277 (276/998, GoNL)
A=0.240 (144/600, NorthernSweden)
A=0.002 (1/534, MGP)
A=0.207 (68/328, HapMap)
A=0.153 (33/216, Qatari)
A=0.199 (43/216, Vietnamese)
G=0.413 (86/208, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
G=0.42 (5/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PITRM1 : Intron Variant
PITRM1-AS1 : Intron Variant
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 G=0.76215 A=0.23785
European Sub 14286 G=0.73919 A=0.26081
African Sub 2946 G=0.8445 A=0.1555
African Others Sub 114 G=0.842 A=0.158
African American Sub 2832 G=0.8446 A=0.1554
Asian Sub 112 G=0.804 A=0.196
East Asian Sub 86 G=0.86 A=0.14
Other Asian Sub 26 G=0.62 A=0.38
Latin American 1 Sub 146 G=0.856 A=0.144
Latin American 2 Sub 610 G=0.848 A=0.152
South Asian Sub 98 G=0.73 A=0.27
Other Sub 692 G=0.788 A=0.212


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 G=0.777215 A=0.222785
gnomAD - Genomes Global Study-wide 140080 G=0.776578 A=0.223422
gnomAD - Genomes European Sub 75878 G=0.73966 A=0.26034
gnomAD - Genomes African Sub 41970 G=0.84203 A=0.15797
gnomAD - Genomes American Sub 13638 G=0.78685 A=0.21315
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.7544 A=0.2456
gnomAD - Genomes East Asian Sub 3124 G=0.7654 A=0.2346
gnomAD - Genomes Other Sub 2148 G=0.7872 A=0.2128
14KJPN JAPANESE Study-wide 28258 G=0.77829 A=0.22171
Allele Frequency Aggregator Total Global 18890 G=0.76215 A=0.23785
Allele Frequency Aggregator European Sub 14286 G=0.73919 A=0.26081
Allele Frequency Aggregator African Sub 2946 G=0.8445 A=0.1555
Allele Frequency Aggregator Other Sub 692 G=0.788 A=0.212
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.848 A=0.152
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.856 A=0.144
Allele Frequency Aggregator Asian Sub 112 G=0.804 A=0.196
Allele Frequency Aggregator South Asian Sub 98 G=0.73 A=0.27
8.3KJPN JAPANESE Study-wide 16760 G=0.77446 A=0.22554
1000Genomes_30x Global Study-wide 6404 G=0.8032 A=0.1968
1000Genomes_30x African Sub 1786 G=0.8740 A=0.1260
1000Genomes_30x Europe Sub 1266 G=0.7599 A=0.2401
1000Genomes_30x South Asian Sub 1202 G=0.7596 A=0.2404
1000Genomes_30x East Asian Sub 1170 G=0.7701 A=0.2299
1000Genomes_30x American Sub 980 G=0.823 A=0.177
1000Genomes Global Study-wide 5008 G=0.7995 A=0.2005
1000Genomes African Sub 1322 G=0.8691 A=0.1309
1000Genomes East Asian Sub 1008 G=0.7659 A=0.2341
1000Genomes Europe Sub 1006 G=0.7575 A=0.2425
1000Genomes South Asian Sub 978 G=0.764 A=0.236
1000Genomes American Sub 694 G=0.827 A=0.173
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7712 A=0.2288
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7097 A=0.2903
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7190 A=0.2810
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7710 A=0.2290
Korean Genome Project KOREAN Study-wide 1832 G=0.7669 A=0.2331
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.723 A=0.277
Northern Sweden ACPOP Study-wide 600 G=0.760 A=0.240
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
HapMap Global Study-wide 328 G=0.793 A=0.207
HapMap African Sub 120 G=0.875 A=0.125
HapMap American Sub 120 G=0.767 A=0.233
HapMap Asian Sub 88 G=0.72 A=0.28
Qatari Global Study-wide 216 G=0.847 A=0.153
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.801 A=0.199
SGDP_PRJ Global Study-wide 208 G=0.413 A=0.587
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 12 G=0.42 A=0.58
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 10 NC_000010.11:g.3144115G>A
GRCh37.p13 chr 10 NC_000010.10:g.3186307G>A
PITRM1 RefSeqGene NG_052908.1:g.33727C>T
Gene: PITRM1, pitrilysin metallopeptidase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PITRM1 transcript variant 1 NM_001242307.2:c.2535+177…

NM_001242307.2:c.2535+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 3 NM_001242309.1:c.2238+177…

NM_001242309.1:c.2238+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 4 NM_001347725.2:c.2334+177…

NM_001347725.2:c.2334+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 5 NM_001347726.2:c.1719+177…

NM_001347726.2:c.1719+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 6 NM_001347727.2:c.1917+177…

NM_001347727.2:c.1917+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 7 NM_001347728.2:c.1227+177…

NM_001347728.2:c.1227+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 8 NM_001347729.1:c.2508+177…

NM_001347729.1:c.2508+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 9 NM_001347730.1:c.2310+177…

NM_001347730.1:c.2310+177C>T

 		N/A Intron Variant
PITRM1 transcript variant 2 NM_014889.4:c.2532+177C>T N/A Intron Variant
PITRM1 transcript variant 10 NR_144638.2:n. N/A Intron Variant
PITRM1 transcript variant 11 NR_144639.2:n. N/A Intron Variant
PITRM1 transcript variant 12 NR_144640.2:n. N/A Intron Variant
PITRM1 transcript variant 13 NR_144641.2:n. N/A Intron Variant
PITRM1 transcript variant X1 XM_047424445.1:c. N/A Genic Downstream Transcript Variant
PITRM1 transcript variant X2 XM_047424446.1:c. N/A Genic Downstream Transcript Variant
Gene: PITRM1-AS1, PITRM1 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PITRM1-AS1 transcript NR_038284.1:n. 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 G= A
GRCh38.p14 chr 10 NC_000010.11:g.3144115= NC_000010.11:g.3144115G>A
GRCh37.p13 chr 10 NC_000010.10:g.3186307= NC_000010.10:g.3186307G>A
PITRM1 RefSeqGene NG_052908.1:g.33727= NG_052908.1:g.33727C>T
PITRM1 transcript variant 1 NM_001242307.1:c.2535+177= NM_001242307.1:c.2535+177C>T
PITRM1 transcript variant 1 NM_001242307.2:c.2535+177= NM_001242307.2:c.2535+177C>T
PITRM1 transcript variant 3 NM_001242309.1:c.2238+177= NM_001242309.1:c.2238+177C>T
PITRM1 transcript variant 4 NM_001347725.2:c.2334+177= NM_001347725.2:c.2334+177C>T
PITRM1 transcript variant 5 NM_001347726.2:c.1719+177= NM_001347726.2:c.1719+177C>T
PITRM1 transcript variant 6 NM_001347727.2:c.1917+177= NM_001347727.2:c.1917+177C>T
PITRM1 transcript variant 7 NM_001347728.2:c.1227+177= NM_001347728.2:c.1227+177C>T
PITRM1 transcript variant 8 NM_001347729.1:c.2508+177= NM_001347729.1:c.2508+177C>T
PITRM1 transcript variant 9 NM_001347730.1:c.2310+177= NM_001347730.1:c.2310+177C>T
PITRM1 transcript variant 2 NM_014889.3:c.2532+177= NM_014889.3:c.2532+177C>T
PITRM1 transcript variant 2 NM_014889.4:c.2532+177= NM_014889.4:c.2532+177C>T
PITRM1 transcript variant X1 XM_005252345.1:c.2334+177= XM_005252345.1:c.2334+177C>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#.

64 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4938831 Aug 28, 2002 (107)
2 SI_EXO ss76898672 Dec 06, 2007 (129)
3 HGSV ss82919819 Dec 14, 2007 (130)
4 BCMHGSC_JDW ss88069293 Mar 23, 2008 (129)
5 1000GENOMES ss109170558 Jan 23, 2009 (130)
6 1000GENOMES ss115264046 Jan 25, 2009 (130)
7 ENSEMBL ss131645137 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss168899341 Jul 04, 2010 (132)
9 BUSHMAN ss201060080 Jul 04, 2010 (132)
10 1000GENOMES ss224528624 Jul 14, 2010 (132)
11 1000GENOMES ss235024960 Jul 15, 2010 (132)
12 1000GENOMES ss241763488 Jul 15, 2010 (132)
13 GMI ss280452456 May 04, 2012 (137)
14 TISHKOFF ss561726996 Apr 25, 2013 (138)
15 SSMP ss656230828 Apr 25, 2013 (138)
16 EVA-GONL ss987127922 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1076709260 Aug 21, 2014 (142)
18 1000GENOMES ss1336024265 Aug 21, 2014 (142)
19 DDI ss1426198724 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1574864647 Apr 01, 2015 (144)
21 EVA_DECODE ss1596774349 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1623855312 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1666849345 Apr 01, 2015 (144)
24 EVA_MGP ss1711245922 Apr 01, 2015 (144)
25 HAMMER_LAB ss1806225143 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1930447789 Feb 12, 2016 (147)
27 GENOMED ss1967041995 Jul 19, 2016 (147)
28 JJLAB ss2025945709 Sep 14, 2016 (149)
29 USC_VALOUEV ss2154186974 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2172154288 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2627441252 Nov 08, 2017 (151)
32 GRF ss2698409196 Nov 08, 2017 (151)
33 GNOMAD ss2884820894 Nov 08, 2017 (151)
34 SWEGEN ss3005830286 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3026755404 Nov 08, 2017 (151)
36 CSHL ss3348926967 Nov 08, 2017 (151)
37 EGCUT_WGS ss3673359165 Jul 13, 2019 (153)
38 EVA_DECODE ss3689152211 Jul 13, 2019 (153)
39 ACPOP ss3737000080 Jul 13, 2019 (153)
40 EVA ss3747664545 Jul 13, 2019 (153)
41 PACBIO ss3786561438 Jul 13, 2019 (153)
42 PACBIO ss3791756164 Jul 13, 2019 (153)
43 PACBIO ss3796637941 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3813027815 Jul 13, 2019 (153)
45 EVA ss3831931079 Apr 26, 2020 (154)
46 EVA ss3839494996 Apr 26, 2020 (154)
47 EVA ss3844960715 Apr 26, 2020 (154)
48 SGDP_PRJ ss3873394520 Apr 26, 2020 (154)
49 KRGDB ss3921326712 Apr 26, 2020 (154)
50 KOGIC ss3967079389 Apr 26, 2020 (154)
51 TOPMED ss4840396870 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5195977667 Apr 26, 2021 (155)
53 1000G_HIGH_COVERAGE ss5282695909 Oct 16, 2022 (156)
54 EVA ss5391192208 Oct 16, 2022 (156)
55 HUGCELL_USP ss5478496900 Oct 16, 2022 (156)
56 1000G_HIGH_COVERAGE ss5575981375 Oct 16, 2022 (156)
57 SANFORD_IMAGENETICS ss5648546694 Oct 16, 2022 (156)
58 TOMMO_GENOMICS ss5740743066 Oct 16, 2022 (156)
59 EVA ss5800156942 Oct 16, 2022 (156)
60 YY_MCH ss5811136609 Oct 16, 2022 (156)
61 EVA ss5823884866 Oct 16, 2022 (156)
62 EVA ss5849407296 Oct 16, 2022 (156)
63 EVA ss5877483697 Oct 16, 2022 (156)
64 EVA ss5939826871 Oct 16, 2022 (156)
65 1000Genomes NC_000010.10 - 3186307 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000010.11 - 3144115 Oct 16, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 3186307 Oct 12, 2018 (152)
68 Genetic variation in the Estonian population NC_000010.10 - 3186307 Oct 12, 2018 (152)
69 The Danish reference pan genome NC_000010.10 - 3186307 Apr 26, 2020 (154)
70 gnomAD - Genomes NC_000010.11 - 3144115 Apr 26, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000010.10 - 3186307 Apr 26, 2020 (154)
72 HapMap NC_000010.11 - 3144115 Apr 26, 2020 (154)
73 KOREAN population from KRGDB NC_000010.10 - 3186307 Apr 26, 2020 (154)
74 Korean Genome Project NC_000010.11 - 3144115 Apr 26, 2020 (154)
75 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 3186307 Apr 26, 2020 (154)
76 Northern Sweden NC_000010.10 - 3186307 Jul 13, 2019 (153)
77 Qatari NC_000010.10 - 3186307 Apr 26, 2020 (154)
78 SGDP_PRJ NC_000010.10 - 3186307 Apr 26, 2020 (154)
79 Siberian NC_000010.10 - 3186307 Apr 26, 2020 (154)
80 8.3KJPN NC_000010.10 - 3186307 Apr 26, 2021 (155)
81 14KJPN NC_000010.11 - 3144115 Oct 16, 2022 (156)
82 TopMed NC_000010.11 - 3144115 Apr 26, 2021 (155)
83 UK 10K study - Twins NC_000010.10 - 3186307 Oct 12, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000010.10 - 3186307 Jul 13, 2019 (153)
85 ALFA NC_000010.11 - 3144115 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)
rs57244705 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82919819 NC_000010.8:3176306:G:A NC_000010.11:3144114:G:A (self)
ss88069293, ss109170558, ss115264046, ss168899341, ss201060080, ss280452456, ss1596774349 NC_000010.9:3176306:G:A NC_000010.11:3144114:G:A (self)
48361980, 26870157, 19097413, 2000795, 11983734, 28504106, 361682, 10284945, 12489719, 25411500, 6703328, 53946974, 26870157, 5963418, ss224528624, ss235024960, ss241763488, ss561726996, ss656230828, ss987127922, ss1076709260, ss1336024265, ss1426198724, ss1574864647, ss1623855312, ss1666849345, ss1711245922, ss1806225143, ss1930447789, ss1967041995, ss2025945709, ss2154186974, ss2627441252, ss2698409196, ss2884820894, ss3005830286, ss3348926967, ss3673359165, ss3737000080, ss3747664545, ss3786561438, ss3791756164, ss3796637941, ss3831931079, ss3839494996, ss3873394520, ss3921326712, ss5195977667, ss5391192208, ss5648546694, ss5800156942, ss5823884866, ss5939826871 NC_000010.10:3186306:G:A NC_000010.11:3144114:G:A (self)
63507310, 341695466, 323522, 23457390, 74580170, 55942525, 15252486450, ss2172154288, ss3026755404, ss3689152211, ss3813027815, ss3844960715, ss3967079389, ss4840396870, ss5282695909, ss5478496900, ss5575981375, ss5740743066, ss5811136609, ss5849407296, ss5877483697 NC_000010.11:3144114:G:A NC_000010.11:3144114:G:A (self)
ss4938831, ss131645137 NT_008705.16:3126306:G:A NC_000010.11:3144114:G:A (self)
ss76898672 NT_077567.3:3126306:G:A NC_000010.11:3144114:G:A (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 rs3752802

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