Name: rs273867
Published: September 21, 2022
License: Open Access

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.

rs273867

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:96798826 (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=0.268756 (71137/264690, TOPMED)
G=0.259399 (36349/140128, GnomAD)
G=0.41867 (11830/28256, 14KJPN) (+ 17 more)
G=0.28269 (5340/18890, ALFA)
G=0.41742 (6996/16760, 8.3KJPN)
G=0.3100 (1985/6404, 1000G_30x)
G=0.3173 (1589/5008, 1000G)
G=0.2710 (1214/4480, Estonian)
G=0.3352 (1292/3854, ALSPAC)
G=0.3395 (1259/3708, TWINSUK)
G=0.4218 (1236/2930, KOREAN)
G=0.4258 (780/1832, Korea1K)
G=0.315 (314/998, GoNL)
G=0.310 (186/600, NorthernSweden)
G=0.233 (76/326, HapMap)
A=0.331 (106/320, SGDP_PRJ)
G=0.167 (36/216, Qatari)
A=0.491 (105/214, Vietnamese)
G=0.38 (15/40, GENOME_DK)
A=0.42 (10/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PTBP2 : 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	A=0.71731	G=0.28269
European	Sub	14286	A=0.68053	G=0.31947
African	Sub	2946	A=0.9168	G=0.0832
African Others	Sub	114	A=0.965	G=0.035
African American	Sub	2832	A=0.9149	G=0.0851
Asian	Sub	112	A=0.527	G=0.473
East Asian	Sub	86	A=0.53	G=0.47
Other Asian	Sub	26	A=0.50	G=0.50
Latin American 1	Sub	146	A=0.781	G=0.219
Latin American 2	Sub	610	A=0.669	G=0.331
South Asian	Sub	98	A=0.61	G=0.39
Other	Sub	692	A=0.702	G=0.298

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.731244	G=0.268756
gnomAD - Genomes	Global	Study-wide	140128	A=0.740601	G=0.259399
gnomAD - Genomes	European	Sub	75868	A=0.67583	G=0.32417
gnomAD - Genomes	African	Sub	42028	A=0.91594	G=0.08406
gnomAD - Genomes	American	Sub	13636	A=0.64880	G=0.35120
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.6165	G=0.3835
gnomAD - Genomes	East Asian	Sub	3124	A=0.5230	G=0.4770
gnomAD - Genomes	Other	Sub	2150	A=0.6888	G=0.3112
14KJPN	JAPANESE	Study-wide	28256	A=0.58133	G=0.41867
Allele Frequency Aggregator	Total	Global	18890	A=0.71731	G=0.28269
Allele Frequency Aggregator	European	Sub	14286	A=0.68053	G=0.31947
Allele Frequency Aggregator	African	Sub	2946	A=0.9168	G=0.0832
Allele Frequency Aggregator	Other	Sub	692	A=0.702	G=0.298
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.669	G=0.331
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.781	G=0.219
Allele Frequency Aggregator	Asian	Sub	112	A=0.527	G=0.473
Allele Frequency Aggregator	South Asian	Sub	98	A=0.61	G=0.39
8.3KJPN	JAPANESE	Study-wide	16760	A=0.58258	G=0.41742
1000Genomes_30x	Global	Study-wide	6404	A=0.6900	G=0.3100
1000Genomes_30x	African	Sub	1786	A=0.9642	G=0.0358
1000Genomes_30x	Europe	Sub	1266	A=0.6754	G=0.3246
1000Genomes_30x	South Asian	Sub	1202	A=0.5083	G=0.4917
1000Genomes_30x	East Asian	Sub	1170	A=0.5393	G=0.4607
1000Genomes_30x	American	Sub	980	A=0.612	G=0.388
1000Genomes	Global	Study-wide	5008	A=0.6827	G=0.3173
1000Genomes	African	Sub	1322	A=0.9637	G=0.0363
1000Genomes	East Asian	Sub	1008	A=0.5456	G=0.4544
1000Genomes	Europe	Sub	1006	A=0.6750	G=0.3250
1000Genomes	South Asian	Sub	978	A=0.503	G=0.497
1000Genomes	American	Sub	694	A=0.611	G=0.389
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7290	G=0.2710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.6648	G=0.3352
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6605	G=0.3395
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5782	G=0.4218
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5742	G=0.4258
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.685	G=0.315
Northern Sweden	ACPOP	Study-wide	600	A=0.690	G=0.310
HapMap	Global	Study-wide	326	A=0.767	G=0.233
HapMap	African	Sub	118	A=0.992	G=0.008
HapMap	American	Sub	118	A=0.686	G=0.314
HapMap	Asian	Sub	90	A=0.58	G=0.42
SGDP_PRJ	Global	Study-wide	320	A=0.331	G=0.669
Qatari	Global	Study-wide	216	A=0.833	G=0.167
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.491	G=0.509
The Danish reference pan genome	Danish	Study-wide	40	A=0.62	G=0.38
Siberian	Global	Study-wide	24	A=0.42	G=0.58

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 1	NC_000001.11:g.96798826A>G
GRCh37.p13 chr 1	NC_000001.10:g.97264382A>G

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.905-5959… NM_001300985.2:c.905-5959A>G	N/A	Intron Variant
PTBP2 transcript variant 2	NM_001300986.2:c.929-5974… NM_001300986.2:c.929-5974A>G	N/A	Intron Variant
PTBP2 transcript variant 3	NM_001300987.2:c.938-5959… NM_001300987.2:c.938-5959A>G	N/A	Intron Variant
PTBP2 transcript variant 4	NM_001300988.2:c.905-5959… NM_001300988.2:c.905-5959A>G	N/A	Intron Variant
PTBP2 transcript variant 5	NM_001300989.2:c.905-5974… NM_001300989.2:c.905-5974A>G	N/A	Intron Variant
PTBP2 transcript variant 7	NM_001300990.2:c.749-5974… NM_001300990.2:c.749-5974A>G	N/A	Intron Variant
PTBP2 transcript variant 6	NM_021190.4:c.905-5974A>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 X2	XM_011541874.3:c.929-5959… XM_011541874.3:c.929-5959A>G	N/A	Intron Variant
PTBP2 transcript variant X3	XM_011541875.3:c.929-5974… XM_011541875.3:c.929-5974A>G	N/A	Intron Variant
PTBP2 transcript variant X1	XM_011541876.3:c.929-5959… XM_011541876.3:c.929-5959A>G	N/A	Intron Variant
PTBP2 transcript variant X6	XM_017001951.2:c.938-5959… XM_017001951.2:c.938-5959A>G	N/A	Intron Variant
PTBP2 transcript variant X3	XM_047426537.1:c.812-5959… XM_047426537.1:c.812-5959A>G	N/A	Intron Variant
PTBP2 transcript variant X4	XM_047426538.1:c.929-5959… XM_047426538.1:c.929-5959A>G	N/A	Intron Variant
PTBP2 transcript variant X5	XM_047426539.1:c.929-5974… XM_047426539.1:c.929-5974A>G	N/A	Intron Variant

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

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 1	NC_000001.11:g.96798826=	NC_000001.11:g.96798826A>G
GRCh37.p13 chr 1	NC_000001.10:g.97264382=	NC_000001.10:g.97264382A>G
PTBP2 transcript variant 1	NM_001300985.2:c.905-5959=	NM_001300985.2:c.905-5959A>G
PTBP2 transcript variant 2	NM_001300986.2:c.929-5974=	NM_001300986.2:c.929-5974A>G
PTBP2 transcript variant 3	NM_001300987.2:c.938-5959=	NM_001300987.2:c.938-5959A>G
PTBP2 transcript variant 4	NM_001300988.2:c.905-5959=	NM_001300988.2:c.905-5959A>G
PTBP2 transcript variant 5	NM_001300989.2:c.905-5974=	NM_001300989.2:c.905-5974A>G
PTBP2 transcript variant 7	NM_001300990.2:c.749-5974=	NM_001300990.2:c.749-5974A>G
PTBP2 transcript	NM_021190.2:c.905-5974=	NM_021190.2:c.905-5974A>G
PTBP2 transcript variant 6	NM_021190.4:c.905-5974=	NM_021190.4:c.905-5974A>G
PTBP2 transcript variant X1	XM_005271084.1:c.905-5959=	XM_005271084.1:c.905-5959A>G
PTBP2 transcript variant X2	XM_005271085.1:c.905-5959=	XM_005271085.1:c.905-5959A>G
PTBP2 transcript variant X3	XM_005271086.1:c.905-5974=	XM_005271086.1:c.905-5974A>G
PTBP2 transcript variant X2	XM_011541874.3:c.929-5959=	XM_011541874.3:c.929-5959A>G
PTBP2 transcript variant X3	XM_011541875.3:c.929-5974=	XM_011541875.3:c.929-5974A>G
PTBP2 transcript variant X1	XM_011541876.3:c.929-5959=	XM_011541876.3:c.929-5959A>G
PTBP2 transcript variant X6	XM_017001951.2:c.938-5959=	XM_017001951.2:c.938-5959A>G
PTBP2 transcript variant X3	XM_047426537.1:c.812-5959=	XM_047426537.1:c.812-5959A>G
PTBP2 transcript variant X4	XM_047426538.1:c.929-5959=	XM_047426538.1:c.929-5959A>G
PTBP2 transcript variant X5	XM_047426539.1:c.929-5974=	XM_047426539.1:c.929-5974A>G

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#.

63 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss355819	Jul 12, 2000 (79)
2	SC_JCM	ss838340	Aug 11, 2000 (87)
3	KWOK	ss1132006	Oct 04, 2000 (86)
4	KWOK	ss1132739	Oct 04, 2000 (86)
5	KWOK	ss1133197	Oct 04, 2000 (86)
6	KWOK	ss1794721	Oct 18, 2000 (92)
7	KWOK	ss1795126	Oct 18, 2000 (87)
8	ABI	ss41074650	Mar 15, 2006 (126)
9	KRIBB_YJKIM	ss80750581	Dec 15, 2007 (130)
10	1000GENOMES	ss108438149	Jan 23, 2009 (130)
11	GMI	ss155389569	Dec 01, 2009 (131)
12	1000GENOMES	ss230649285	Jul 14, 2010 (132)
13	1000GENOMES	ss238318412	Jul 15, 2010 (132)
14	GMI	ss275938754	May 04, 2012 (137)
15	TISHKOFF	ss554462950	Apr 25, 2013 (138)
16	SSMP	ss648240927	Apr 25, 2013 (138)
17	EVA-GONL	ss975462456	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1068113191	Aug 21, 2014 (142)
19	1000GENOMES	ss1292031204	Aug 21, 2014 (142)
20	DDI	ss1425906139	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1574256555	Apr 01, 2015 (144)
22	EVA_DECODE	ss1584839709	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1600775211	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1643769244	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1794782741	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918663205	Feb 12, 2016 (147)
27	GENOMED	ss1966816428	Jul 19, 2016 (147)
28	JJLAB	ss2019852908	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2147871720	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2164864943	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2624438363	Nov 08, 2017 (151)
32	GRF	ss2697798807	Nov 08, 2017 (151)
33	GNOMAD	ss2758414893	Nov 08, 2017 (151)
34	SWEGEN	ss2987275180	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3023690118	Nov 08, 2017 (151)
36	CSHL	ss3343587294	Nov 08, 2017 (151)
37	URBANLAB	ss3646727772	Oct 11, 2018 (152)
38	EGCUT_WGS	ss3655357208	Jul 12, 2019 (153)
39	EVA_DECODE	ss3687330103	Jul 12, 2019 (153)
40	ACPOP	ss3727297336	Jul 12, 2019 (153)
41	EVA	ss3746551596	Jul 12, 2019 (153)
42	PACBIO	ss3783491562	Jul 12, 2019 (153)
43	PACBIO	ss3789137328	Jul 12, 2019 (153)
44	PACBIO	ss3794010167	Jul 12, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3799553358	Jul 12, 2019 (153)
46	EVA	ss3826317463	Apr 25, 2020 (154)
47	SGDP_PRJ	ss3849439420	Apr 25, 2020 (154)
48	KRGDB	ss3894512896	Apr 25, 2020 (154)
49	KOGIC	ss3945057609	Apr 25, 2020 (154)
50	TOPMED	ss4459982571	Apr 25, 2021 (155)
51	TOMMO_GENOMICS	ss5145228126	Apr 25, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5243257050	Oct 12, 2022 (156)
53	EVA	ss5320549113	Oct 12, 2022 (156)
54	HUGCELL_USP	ss5444215406	Oct 12, 2022 (156)
55	EVA	ss5505959046	Oct 12, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5516061159	Oct 12, 2022 (156)
57	SANFORD_IMAGENETICS	ss5626095569	Oct 12, 2022 (156)
58	TOMMO_GENOMICS	ss5670363931	Oct 12, 2022 (156)
59	YY_MCH	ss5800844347	Oct 12, 2022 (156)
60	EVA	ss5832346285	Oct 12, 2022 (156)
61	EVA	ss5849026438	Oct 12, 2022 (156)
62	EVA	ss5909397056	Oct 12, 2022 (156)
63	EVA	ss5937953344	Oct 12, 2022 (156)
64	1000Genomes	NC_000001.10 - 97264382	Oct 11, 2018 (152)
65	1000Genomes_30x	NC_000001.11 - 96798826	Oct 12, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 97264382	Oct 11, 2018 (152)
67	Genetic variation in the Estonian population	NC_000001.10 - 97264382	Oct 11, 2018 (152)
68	The Danish reference pan genome	NC_000001.10 - 97264382	Apr 25, 2020 (154)
69	gnomAD - Genomes	NC_000001.11 - 96798826	Apr 25, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000001.10 - 97264382	Apr 25, 2020 (154)
71	HapMap	NC_000001.11 - 96798826	Apr 25, 2020 (154)
72	KOREAN population from KRGDB	NC_000001.10 - 97264382	Apr 25, 2020 (154)
73	Korean Genome Project	NC_000001.11 - 96798826	Apr 25, 2020 (154)
74	Northern Sweden	NC_000001.10 - 97264382	Jul 12, 2019 (153)
75	Qatari	NC_000001.10 - 97264382	Apr 25, 2020 (154)
76	SGDP_PRJ	NC_000001.10 - 97264382	Apr 25, 2020 (154)
77	Siberian	NC_000001.10 - 97264382	Apr 25, 2020 (154)
78	8.3KJPN	NC_000001.10 - 97264382	Apr 25, 2021 (155)
79	14KJPN	NC_000001.11 - 96798826	Oct 12, 2022 (156)
80	TopMed	NC_000001.11 - 96798826	Apr 25, 2021 (155)
81	UK 10K study - Twins	NC_000001.10 - 97264382	Oct 11, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000001.10 - 97264382	Jul 12, 2019 (153)
83	ALFA	NC_000001.11 - 96798826	Apr 25, 2021 (155)

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)
rs665078	Oct 23, 2000 (87)
rs1223065	Jan 18, 2001 (92)
rs60966630	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss108438149, ss275938754, ss1584839709	NC_000001.9:97036969:A:G	NC_000001.11:96798825:A:G	(self)
2792202, 1538364, 1095456, 1620856, 666944, 1690290, 582201, 705135, 1456400, 388074, 3197433, 1538364, 331048, ss230649285, ss238318412, ss554462950, ss648240927, ss975462456, ss1068113191, ss1292031204, ss1425906139, ss1574256555, ss1600775211, ss1643769244, ss1794782741, ss1918663205, ss1966816428, ss2019852908, ss2147871720, ss2624438363, ss2697798807, ss2758414893, ss2987275180, ss3343587294, ss3655357208, ss3727297336, ss3746551596, ss3783491562, ss3789137328, ss3794010167, ss3826317463, ss3849439420, ss3894512896, ss5145228126, ss5320549113, ss5505959046, ss5626095569, ss5832346285, ss5937953344	NC_000001.10:97264381:A:G	NC_000001.11:96798825:A:G	(self)
3587094, 19722529, 132510, 1435610, 4201035, 23588906, 4838637547, ss2164864943, ss3023690118, ss3646727772, ss3687330103, ss3799553358, ss3945057609, ss4459982571, ss5243257050, ss5444215406, ss5516061159, ss5670363931, ss5800844347, ss5849026438, ss5909397056	NC_000001.11:96798825:A:G	NC_000001.11:96798825:A:G	(self)
ss355819, ss838340, ss1132006, ss1132739, ss1133197, ss1794721, ss1795126, ss41074650, ss80750581, ss155389569	NT_032977.9:67236299:A:G	NC_000001.11:96798825:A:G	(self)

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

No publications for rs273867

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs273867