Name: rs12942969
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.

rs12942969

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:58815511 (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=0.231580 (61297/264690, TOPMED)
T=0.242103 (33909/140060, GnomAD)
T=0.26865 (4487/16702, ALFA) (+ 15 more)
T=0.1485 (951/6404, 1000G_30x)
T=0.1462 (732/5008, 1000G)
T=0.2717 (1217/4480, Estonian)
T=0.3194 (1231/3854, ALSPAC)
T=0.3234 (1199/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.328 (327/998, GoNL)
T=0.335 (201/600, NorthernSweden)
T=0.310 (67/216, Qatari)
T=0.009 (2/214, Vietnamese)
A=0.466 (55/118, SGDP_PRJ)
T=0.00 (0/78, HapMap)
T=0.12 (5/40, GENOME_DK)
A=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PPM1E : 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	16702	A=0.73135	T=0.26865
European	Sub	12214	A=0.68315	T=0.31685
African	Sub	2864	A=0.8935	T=0.1065
African Others	Sub	108	A=0.935	T=0.065
African American	Sub	2756	A=0.8919	T=0.1081
Asian	Sub	108	A=1.000	T=0.000
East Asian	Sub	84	A=1.00	T=0.00
Other Asian	Sub	24	A=1.00	T=0.00
Latin American 1	Sub	146	A=0.767	T=0.233
Latin American 2	Sub	610	A=0.803	T=0.197
South Asian	Sub	94	A=0.83	T=0.17
Other	Sub	666	A=0.787	T=0.213

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=0.768420	T=0.231580
gnomAD - Genomes	Global	Study-wide	140060	A=0.757897	T=0.242103
gnomAD - Genomes	European	Sub	75832	A=0.68134	T=0.31866
gnomAD - Genomes	African	Sub	41988	A=0.88956	T=0.11044
gnomAD - Genomes	American	Sub	13638	A=0.76793	T=0.23207
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.5966	T=0.4034
gnomAD - Genomes	East Asian	Sub	3132	A=0.9974	T=0.0026
gnomAD - Genomes	Other	Sub	2148	A=0.7235	T=0.2765
Allele Frequency Aggregator	Total	Global	16702	A=0.73135	T=0.26865
Allele Frequency Aggregator	European	Sub	12214	A=0.68315	T=0.31685
Allele Frequency Aggregator	African	Sub	2864	A=0.8935	T=0.1065
Allele Frequency Aggregator	Other	Sub	666	A=0.787	T=0.213
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.803	T=0.197
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.767	T=0.233
Allele Frequency Aggregator	Asian	Sub	108	A=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	A=0.83	T=0.17
1000Genomes_30x	Global	Study-wide	6404	A=0.8515	T=0.1485
1000Genomes_30x	African	Sub	1786	A=0.9087	T=0.0913
1000Genomes_30x	Europe	Sub	1266	A=0.6509	T=0.3491
1000Genomes_30x	South Asian	Sub	1202	A=0.8611	T=0.1389
1000Genomes_30x	East Asian	Sub	1170	A=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	A=0.817	T=0.183
1000Genomes	Global	Study-wide	5008	A=0.8538	T=0.1462
1000Genomes	African	Sub	1322	A=0.9107	T=0.0893
1000Genomes	East Asian	Sub	1008	A=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	A=0.6471	T=0.3529
1000Genomes	South Asian	Sub	978	A=0.864	T=0.136
1000Genomes	American	Sub	694	A=0.818	T=0.182
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7283	T=0.2717
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.6806	T=0.3194
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6766	T=0.3234
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9997	T=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.672	T=0.328
Northern Sweden	ACPOP	Study-wide	600	A=0.665	T=0.335
Qatari	Global	Study-wide	216	A=0.690	T=0.310
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.991	T=0.009
SGDP_PRJ	Global	Study-wide	118	A=0.466	T=0.534
HapMap	Global	Study-wide	78	A=1.00	T=0.00
HapMap	Asian	Sub	78	A=1.00	T=0.00
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	T=0.12
Siberian	Global	Study-wide	10	A=0.5	T=0.5

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 17	NC_000017.11:g.58815511A>T
GRCh37.p13 chr 17	NC_000017.10:g.56892872A>T

Gene: PPM1E, protein phosphatase, Mg2+/Mn2+ dependent 1E (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PPM1E transcript variant 1	NM_014906.5:c.464+59050A>T	N/A	Intron Variant
PPM1E transcript variant 2	NR_048561.1:n.	N/A	Intron Variant
PPM1E transcript variant X1	XM_024450657.2:c.	N/A	Genic Upstream Transcript Variant
PPM1E transcript variant X2	XM_047435630.1:c.	N/A	Genic Upstream Transcript 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=	T
GRCh38.p14 chr 17	NC_000017.11:g.58815511=	NC_000017.11:g.58815511A>T
GRCh37.p13 chr 17	NC_000017.10:g.56892872=	NC_000017.10:g.56892872A>T
PPM1E transcript variant 1	NM_014906.4:c.464+59050=	NM_014906.4:c.464+59050A>T
PPM1E transcript variant 1	NM_014906.5:c.464+59050=	NM_014906.5:c.464+59050A>T
PPM1E transcript variant X1	XM_005257168.1:c.-48+59050=	XM_005257168.1:c.-48+59050A>T

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#.

53 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21398591	Apr 05, 2004 (121)
2	ABI	ss43970635	Mar 15, 2006 (126)
3	BCMHGSC_JDW	ss90627929	Mar 24, 2008 (129)
4	HUMANGENOME_JCVI	ss96603318	Feb 02, 2009 (130)
5	1000GENOMES	ss109841942	Jan 24, 2009 (130)
6	ENSEMBL	ss132622746	Dec 01, 2009 (131)
7	ENSEMBL	ss137130878	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss168352119	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss171587099	Jul 04, 2010 (132)
10	1000GENOMES	ss227600335	Jul 14, 2010 (132)
11	1000GENOMES	ss237283756	Jul 15, 2010 (132)
12	PJP	ss291974919	May 09, 2011 (134)
13	TISHKOFF	ss565338234	Apr 25, 2013 (138)
14	SSMP	ss661147202	Apr 25, 2013 (138)
15	EVA-GONL	ss993219806	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1081135189	Aug 21, 2014 (142)
17	1000GENOMES	ss1359090106	Aug 21, 2014 (142)
18	DDI	ss1428065223	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1578201504	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1635873362	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1678867395	Apr 01, 2015 (144)
22	EVA_DECODE	ss1697266478	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1936680391	Feb 12, 2016 (147)
24	GENOMED	ss1968412792	Jul 19, 2016 (147)
25	JJLAB	ss2029115754	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2157594135	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2217725208	Dec 20, 2016 (150)
28	GNOMAD	ss2951150917	Nov 08, 2017 (151)
29	AFFY	ss2985735668	Nov 08, 2017 (151)
30	SWEGEN	ss3015717551	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3028380448	Nov 08, 2017 (151)
32	CSHL	ss3351791666	Nov 08, 2017 (151)
33	URBANLAB	ss3650679073	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3682595337	Jul 13, 2019 (153)
35	EVA_DECODE	ss3700687171	Jul 13, 2019 (153)
36	ACPOP	ss3742120686	Jul 13, 2019 (153)
37	EVA	ss3754798663	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3820063351	Jul 13, 2019 (153)
39	EVA	ss3834922397	Apr 27, 2020 (154)
40	EVA	ss3841074104	Apr 27, 2020 (154)
41	EVA	ss3846571406	Apr 27, 2020 (154)
42	SGDP_PRJ	ss3885979260	Apr 27, 2020 (154)
43	KRGDB	ss3935709195	Apr 27, 2020 (154)
44	TOPMED	ss5039847636	Apr 27, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5303521760	Oct 16, 2022 (156)
46	EVA	ss5428297278	Oct 16, 2022 (156)
47	HUGCELL_USP	ss5496530126	Oct 16, 2022 (156)
48	EVA	ss5511799019	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5607433715	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5660319184	Oct 16, 2022 (156)
51	EVA	ss5834133642	Oct 16, 2022 (156)
52	EVA	ss5914372010	Oct 16, 2022 (156)
53	EVA	ss5951714085	Oct 16, 2022 (156)
54	1000Genomes	NC_000017.10 - 56892872	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000017.11 - 58815511	Oct 16, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 56892872	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000017.10 - 56892872	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000017.10 - 56892872	Apr 27, 2020 (154)
59	gnomAD - Genomes	NC_000017.11 - 58815511	Apr 27, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000017.10 - 56892872	Apr 27, 2020 (154)
61	HapMap	NC_000017.11 - 58815511	Apr 27, 2020 (154)
62	KOREAN population from KRGDB	NC_000017.10 - 56892872	Apr 27, 2020 (154)
63	Northern Sweden	NC_000017.10 - 56892872	Jul 13, 2019 (153)
64	Qatari	NC_000017.10 - 56892872	Apr 27, 2020 (154)
65	SGDP_PRJ	NC_000017.10 - 56892872	Apr 27, 2020 (154)
66	Siberian	NC_000017.10 - 56892872	Apr 27, 2020 (154)
67	TopMed	NC_000017.11 - 58815511	Apr 27, 2021 (155)
68	UK 10K study - Twins	NC_000017.10 - 56892872	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000017.10 - 56892872	Jul 13, 2019 (153)
70	ALFA	NC_000017.11 - 58815511	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss90627929, ss109841942, ss168352119, ss171587099, ss291974919, ss1697266478	NC_000017.9:54247870:A:T	NC_000017.11:58815510:A:T	(self)
72348290, 40093667, 28333585, 4402002, 17867037, 42886589, 15405551, 18722313, 37996240, 10110489, 40093667, 8867297, ss227600335, ss237283756, ss565338234, ss661147202, ss993219806, ss1081135189, ss1359090106, ss1428065223, ss1578201504, ss1635873362, ss1678867395, ss1936680391, ss1968412792, ss2029115754, ss2157594135, ss2951150917, ss2985735668, ss3015717551, ss3351791666, ss3682595337, ss3742120686, ss3754798663, ss3834922397, ss3841074104, ss3885979260, ss3935709195, ss5428297278, ss5511799019, ss5660319184, ss5834133642, ss5951714085	NC_000017.10:56892871:A:T	NC_000017.11:58815510:A:T	(self)
94959650, 510502693, 1507925, 255393298, 10088643044, ss2217725208, ss3028380448, ss3650679073, ss3700687171, ss3820063351, ss3846571406, ss5039847636, ss5303521760, ss5496530126, ss5607433715, ss5914372010	NC_000017.11:58815510:A:T	NC_000017.11:58815510:A:T	(self)
ss21398591	NT_010783.14:15546149:A:T	NC_000017.11:58815510:A:T	(self)
ss43970635, ss96603318, ss132622746, ss137130878	NT_010783.15:22167023:A:T	NC_000017.11:58815510:A:T	(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 rs12942969

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12942969