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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.

rs273884

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:96807757 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.292935 (77537/264690, TOPMED)
T=0.282817 (39613/140066, GnomAD)
T=0.29397 (5553/18890, ALFA) (+ 16 more)
T=0.37607 (6303/16760, 8.3KJPN)
T=0.3349 (1677/5008, 1000G)
T=0.2705 (1212/4480, Estonian)
T=0.3332 (1284/3854, ALSPAC)
T=0.3368 (1249/3708, TWINSUK)
T=0.3993 (1170/2930, KOREAN)
T=0.4034 (739/1832, Korea1K)
T=0.315 (314/998, GoNL)
T=0.310 (186/600, NorthernSweden)
A=0.334 (113/338, SGDP_PRJ)
T=0.241 (79/328, HapMap)
T=0.185 (40/216, Qatari)
T=0.495 (105/212, Vietnamese)
T=0.38 (15/40, GENOME_DK)
A=0.42 (10/24, Siberian)
T=0.33 (4/12, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTBP2 : Intron Variant
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 1 NC_000001.11:g.96807757A>G
GRCh38.p13 chr 1 NC_000001.11:g.96807757A>T
GRCh37.p13 chr 1 NC_000001.10:g.97273313A>G
GRCh37.p13 chr 1 NC_000001.10:g.97273313A>T
Gene: PTBP2, polypyrimidine tract binding protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTBP2 transcript variant 1 NM_001300985.2:c.1186+799…

NM_001300985.2:c.1186+799A>G

N/A Intron Variant
PTBP2 transcript variant 2 NM_001300986.2:c.1195+799…

NM_001300986.2:c.1195+799A>G

N/A Intron Variant
PTBP2 transcript variant 3 NM_001300987.2:c.1219+799…

NM_001300987.2:c.1219+799A>G

N/A Intron Variant
PTBP2 transcript variant 4 NM_001300988.2:c.1186+799…

NM_001300988.2:c.1186+799A>G

N/A Intron Variant
PTBP2 transcript variant 5 NM_001300989.2:c.1171+799…

NM_001300989.2:c.1171+799A>G

N/A Intron Variant
PTBP2 transcript variant 7 NM_001300990.2:c.1015+799…

NM_001300990.2:c.1015+799A>G

N/A Intron Variant
PTBP2 transcript variant 6 NM_021190.4:c.1171+799A>G N/A Intron Variant
PTBP2 transcript variant 9 NR_125356.1:n. N/A Intron Variant
PTBP2 transcript variant 8 NR_125357.2:n. N/A Intron Variant
PTBP2 transcript variant X1 XM_011541874.2:c.1210+799…

XM_011541874.2:c.1210+799A>G

N/A Intron Variant
PTBP2 transcript variant X2 XM_011541875.2:c.1195+799…

XM_011541875.2:c.1195+799A>G

N/A Intron Variant
PTBP2 transcript variant X3 XM_011541876.2:c.1210+799…

XM_011541876.2:c.1210+799A>G

N/A Intron Variant
PTBP2 transcript variant X10 XM_017001951.1:c.1219+799…

XM_017001951.1:c.1219+799A>G

N/A Intron Variant
PTBP2 transcript variant X8 XR_001737346.2:n. N/A Intron Variant
PTBP2 transcript variant X9 XR_001737347.2:n. N/A Intron Variant
PTBP2 transcript variant X5 XR_946720.2:n. N/A Intron Variant
PTBP2 transcript variant X4 XR_946721.2:n. N/A Intron Variant
PTBP2 transcript variant X7 XR_946722.2:n. N/A Intron Variant
PTBP2 transcript variant X6 XR_946723.3: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

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 18890 A=0.70603 T=0.29397
European Sub 14286 A=0.68060 T=0.31940
African Sub 2946 A=0.8510 T=0.1490
African Others Sub 114 A=0.895 T=0.105
African American Sub 2832 A=0.8492 T=0.1508
Asian Sub 112 A=0.545 T=0.455
East Asian Sub 86 A=0.55 T=0.45
Other Asian Sub 26 A=0.54 T=0.46
Latin American 1 Sub 146 A=0.760 T=0.240
Latin American 2 Sub 610 A=0.664 T=0.336
South Asian Sub 98 A=0.61 T=0.39
Other Sub 692 A=0.679 T=0.321


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=0.707065 T=0.292935
gnomAD - Genomes Global Study-wide 140066 A=0.717183 T=0.282817
gnomAD - Genomes European Sub 75844 A=0.67561 T=0.32439
gnomAD - Genomes African Sub 41990 A=0.84051 T=0.15949
gnomAD - Genomes American Sub 13630 A=0.64123 T=0.35877
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.6153 T=0.3847
gnomAD - Genomes East Asian Sub 3130 A=0.5450 T=0.4550
gnomAD - Genomes Other Sub 2150 A=0.6647 T=0.3353
8.3KJPN JAPANESE Study-wide 16760 A=0.62393 T=0.37607
1000Genomes Global Study-wide 5008 A=0.6651 T=0.3349
1000Genomes African Sub 1322 A=0.8790 T=0.1210
1000Genomes East Asian Sub 1008 A=0.5734 T=0.4266
1000Genomes Europe Sub 1006 A=0.6750 T=0.3250
1000Genomes South Asian Sub 978 A=0.506 T=0.494
1000Genomes American Sub 694 A=0.601 T=0.399
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7295 T=0.2705
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6668 T=0.3332
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6632 T=0.3368
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6007 G=0.0000, T=0.3993
Korean Genome Project KOREAN Study-wide 1832 A=0.5966 T=0.4034
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.685 T=0.315
Northern Sweden ACPOP Study-wide 600 A=0.690 T=0.310
SGDP_PRJ Global Study-wide 338 A=0.334 T=0.666
HapMap Global Study-wide 328 A=0.759 T=0.241
HapMap African Sub 120 A=0.942 T=0.058
HapMap American Sub 120 A=0.692 T=0.308
HapMap Asian Sub 88 A=0.60 T=0.40
Qatari Global Study-wide 216 A=0.815 T=0.185
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.505 T=0.495
The Danish reference pan genome Danish Study-wide 40 A=0.62 T=0.38
Siberian Global Study-wide 24 A=0.42 T=0.58
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 12 A=0.67 T=0.33
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 T
GRCh38.p13 chr 1 NC_000001.11:g.96807757= NC_000001.11:g.96807757A>G NC_000001.11:g.96807757A>T
GRCh37.p13 chr 1 NC_000001.10:g.97273313= NC_000001.10:g.97273313A>G NC_000001.10:g.97273313A>T
PTBP2 transcript variant 1 NM_001300985.2:c.1186+799= NM_001300985.2:c.1186+799A>G NM_001300985.2:c.1186+799A>T
PTBP2 transcript variant 2 NM_001300986.2:c.1195+799= NM_001300986.2:c.1195+799A>G NM_001300986.2:c.1195+799A>T
PTBP2 transcript variant 3 NM_001300987.2:c.1219+799= NM_001300987.2:c.1219+799A>G NM_001300987.2:c.1219+799A>T
PTBP2 transcript variant 4 NM_001300988.2:c.1186+799= NM_001300988.2:c.1186+799A>G NM_001300988.2:c.1186+799A>T
PTBP2 transcript variant 5 NM_001300989.2:c.1171+799= NM_001300989.2:c.1171+799A>G NM_001300989.2:c.1171+799A>T
PTBP2 transcript variant 7 NM_001300990.2:c.1015+799= NM_001300990.2:c.1015+799A>G NM_001300990.2:c.1015+799A>T
PTBP2 transcript NM_021190.2:c.1171+799= NM_021190.2:c.1171+799A>G NM_021190.2:c.1171+799A>T
PTBP2 transcript variant 6 NM_021190.4:c.1171+799= NM_021190.4:c.1171+799A>G NM_021190.4:c.1171+799A>T
PTBP2 transcript variant X1 XM_005271084.1:c.1186+799= XM_005271084.1:c.1186+799A>G XM_005271084.1:c.1186+799A>T
PTBP2 transcript variant X2 XM_005271085.1:c.1186+799= XM_005271085.1:c.1186+799A>G XM_005271085.1:c.1186+799A>T
PTBP2 transcript variant X3 XM_005271086.1:c.1171+799= XM_005271086.1:c.1171+799A>G XM_005271086.1:c.1171+799A>T
PTBP2 transcript variant X1 XM_011541874.2:c.1210+799= XM_011541874.2:c.1210+799A>G XM_011541874.2:c.1210+799A>T
PTBP2 transcript variant X2 XM_011541875.2:c.1195+799= XM_011541875.2:c.1195+799A>G XM_011541875.2:c.1195+799A>T
PTBP2 transcript variant X3 XM_011541876.2:c.1210+799= XM_011541876.2:c.1210+799A>G XM_011541876.2:c.1210+799A>T
PTBP2 transcript variant X10 XM_017001951.1:c.1219+799= XM_017001951.1:c.1219+799A>G XM_017001951.1:c.1219+799A>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#.

66 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss355837 Jul 12, 2000 (79)
2 SC_JCM ss758313 Aug 11, 2000 (85)
3 KWOK ss1131999 Oct 04, 2000 (86)
4 KWOK ss1132732 Oct 04, 2000 (86)
5 KWOK ss1133183 Oct 04, 2000 (86)
6 TSC-CSHL ss1413663 Oct 04, 2000 (86)
7 KWOK ss1794744 Oct 18, 2000 (87)
8 KWOK ss1795151 Oct 18, 2000 (87)
9 YUSUKE ss4977378 Aug 28, 2002 (108)
10 SC_JCM ss5645223 Feb 20, 2003 (111)
11 PERLEGEN ss23860572 Sep 20, 2004 (123)
12 ABI ss43987279 Mar 14, 2006 (126)
13 ILLUMINA ss65776455 Oct 16, 2006 (127)
14 KRIBB_YJKIM ss80750590 Dec 15, 2007 (130)
15 HUMANGENOME_JCVI ss99231261 Feb 06, 2009 (130)
16 1000GENOMES ss108438165 Jan 23, 2009 (130)
17 ENSEMBL ss138847286 Dec 01, 2009 (131)
18 GMI ss155389600 Dec 01, 2009 (131)
19 BUSHMAN ss198811646 Jul 04, 2010 (132)
20 1000GENOMES ss218539123 Jul 14, 2010 (132)
21 1000GENOMES ss230649306 Jul 14, 2010 (132)
22 1000GENOMES ss238318422 Jul 15, 2010 (132)
23 BL ss253303124 May 09, 2011 (134)
24 GMI ss275938766 May 04, 2012 (137)
25 PJP ss290577201 May 09, 2011 (134)
26 ILLUMINA ss410925480 Sep 17, 2011 (135)
27 TISHKOFF ss554463007 Apr 25, 2013 (138)
28 SSMP ss648240949 Apr 25, 2013 (138)
29 EVA-GONL ss975462505 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1068113212 Aug 21, 2014 (142)
31 1000GENOMES ss1292031405 Aug 21, 2014 (142)
32 DDI ss1425906148 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1574256589 Apr 01, 2015 (144)
34 EVA_DECODE ss1584839761 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1600775311 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1643769344 Apr 01, 2015 (144)
37 HAMMER_LAB ss1794782775 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1918663254 Feb 12, 2016 (147)
39 GENOMED ss1966816437 Jul 19, 2016 (147)
40 JJLAB ss2019852923 Sep 14, 2016 (149)
41 USC_VALOUEV ss2147871738 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2164865440 Dec 20, 2016 (150)
43 TOPMED ss2327211306 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2624438368 Nov 08, 2017 (151)
45 GRF ss2697798836 Nov 08, 2017 (151)
46 GNOMAD ss2758415589 Nov 08, 2017 (151)
47 SWEGEN ss2987275271 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3023690125 Nov 08, 2017 (151)
49 TOPMED ss3084136063 Nov 08, 2017 (151)
50 CSHL ss3343587306 Nov 08, 2017 (151)
51 URBANLAB ss3646727778 Oct 11, 2018 (152)
52 EGCUT_WGS ss3655357309 Jul 12, 2019 (153)
53 EVA_DECODE ss3687330214 Jul 12, 2019 (153)
54 ACPOP ss3727297365 Jul 12, 2019 (153)
55 EVA ss3746551657 Jul 12, 2019 (153)
56 PACBIO ss3783491570 Jul 12, 2019 (153)
57 PACBIO ss3789137335 Jul 12, 2019 (153)
58 PACBIO ss3794010174 Jul 12, 2019 (153)
59 KHV_HUMAN_GENOMES ss3799553411 Jul 12, 2019 (153)
60 EVA ss3826317480 Apr 25, 2020 (154)
61 SGDP_PRJ ss3849439511 Apr 25, 2020 (154)
62 KRGDB ss3894513043 Apr 25, 2020 (154)
63 KOGIC ss3945057700 Apr 25, 2020 (154)
64 EVA ss3984813989 Apr 25, 2021 (155)
65 TOPMED ss4459984808 Apr 25, 2021 (155)
66 TOMMO_GENOMICS ss5145228435 Apr 25, 2021 (155)
67 1000Genomes NC_000001.10 - 97273313 Oct 11, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 97273313 Oct 11, 2018 (152)
69 Genetic variation in the Estonian population NC_000001.10 - 97273313 Oct 11, 2018 (152)
70 The Danish reference pan genome NC_000001.10 - 97273313 Apr 25, 2020 (154)
71 gnomAD - Genomes NC_000001.11 - 96807757 Apr 25, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000001.10 - 97273313 Apr 25, 2020 (154)
73 HapMap NC_000001.11 - 96807757 Apr 25, 2020 (154)
74 KOREAN population from KRGDB NC_000001.10 - 97273313 Apr 25, 2020 (154)
75 Korean Genome Project NC_000001.11 - 96807757 Apr 25, 2020 (154)
76 Northern Sweden NC_000001.10 - 97273313 Jul 12, 2019 (153)
77 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 97273313 Apr 25, 2021 (155)
78 Qatari NC_000001.10 - 97273313 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000001.10 - 97273313 Apr 25, 2020 (154)
80 Siberian NC_000001.10 - 97273313 Apr 25, 2020 (154)
81 8.3KJPN NC_000001.10 - 97273313 Apr 25, 2021 (155)
82 TopMed NC_000001.11 - 96807757 Apr 25, 2021 (155)
83 UK 10K study - Twins NC_000001.10 - 97273313 Oct 11, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000001.10 - 97273313 Jul 12, 2019 (153)
85 ALFA NC_000001.11 - 96807757 Apr 25, 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)
rs586641 Sep 19, 2000 (85)
rs3791008 Oct 08, 2002 (108)
rs60375939 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1690437, ss3894513043 NC_000001.10:97273312:A:G NC_000001.11:96807756:A:G (self)
ss108438165, ss198811646, ss253303124, ss275938766, ss290577201, ss410925480, ss1584839761 NC_000001.9:97045900:A:T NC_000001.11:96807756:A:T (self)
2792414, 1538480, 1095557, 1620868, 666991, 1690437, 582230, 39916, 705184, 1456491, 388092, 3197742, 1538480, 331069, ss218539123, ss230649306, ss238318422, ss554463007, ss648240949, ss975462505, ss1068113212, ss1292031405, ss1425906148, ss1574256589, ss1600775311, ss1643769344, ss1794782775, ss1918663254, ss1966816437, ss2019852923, ss2147871738, ss2327211306, ss2624438368, ss2697798836, ss2758415589, ss2987275271, ss3343587306, ss3655357309, ss3727297365, ss3746551657, ss3783491570, ss3789137335, ss3794010174, ss3826317480, ss3849439511, ss3894513043, ss3984813989, ss5145228435 NC_000001.10:97273312:A:T NC_000001.11:96807756:A:T (self)
19724462, 132518, 1435701, 14857780, 23591143, 4052062874, ss2164865440, ss3023690125, ss3084136063, ss3646727778, ss3687330214, ss3799553411, ss3945057700, ss4459984808 NC_000001.11:96807756:A:T NC_000001.11:96807756:A:T (self)
ss355837, ss758313, ss1131999, ss1132732, ss1133183, ss1413663, ss1794744, ss1795151, ss4977378, ss5645223, ss23860572, ss43987279, ss65776455, ss80750590, ss99231261, ss138847286, ss155389600 NT_032977.9:67245230:A:T NC_000001.11:96807756: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 rs273884

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