Name: rs3892467
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.

rs3892467

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:973693 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.366312 (96959/264690, TOPMED)
T=0.351194 (49170/140008, GnomAD)
C=0.36672 (10362/28256, 14KJPN) (+ 14 more)
T=0.36456 (8320/22822, ALFA)
C=0.36790 (6166/16760, 8.3KJPN)
T=0.4085 (2616/6404, 1000G_30x)
T=0.4179 (2093/5008, 1000G)
T=0.3310 (1483/4480, Estonian)
T=0.3915 (1509/3854, ALSPAC)
T=0.3956 (1467/3708, TWINSUK)
C=0.3675 (1076/2928, KOREAN)
T=0.371 (370/998, GoNL)
T=0.348 (209/600, NorthernSweden)
C=0.354 (126/356, SGDP_PRJ)
T=0.315 (68/216, Qatari)
T=0.33 (13/40, GENOME_DK)
C=0.38 (13/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PLEKHN1 : 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	22822	C=0.63544	G=0.00000, T=0.36456
European	Sub	18362	C=0.61872	G=0.00000, T=0.38128
African	Sub	2760	C=0.7714	G=0.0000, T=0.2286
African Others	Sub	100	C=0.77	G=0.00, T=0.23
African American	Sub	2660	C=0.7714	G=0.0000, T=0.2286
Asian	Sub	112	C=0.357	G=0.000, T=0.643
East Asian	Sub	86	C=0.30	G=0.00, T=0.70
Other Asian	Sub	26	C=0.54	G=0.00, T=0.46
Latin American 1	Sub	146	C=0.699	G=0.000, T=0.301
Latin American 2	Sub	610	C=0.605	G=0.000, T=0.395
South Asian	Sub	98	C=0.53	G=0.00, T=0.47
Other	Sub	734	C=0.612	G=0.000, T=0.388

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	C=0.633688	T=0.366312
gnomAD - Genomes	Global	Study-wide	140008	C=0.648806	T=0.351194
gnomAD - Genomes	European	Sub	75806	C=0.63066	T=0.36934
gnomAD - Genomes	African	Sub	41970	C=0.73881	T=0.26119
gnomAD - Genomes	American	Sub	13642	C=0.59031	T=0.40969
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.4895	T=0.5105
gnomAD - Genomes	East Asian	Sub	3118	C=0.3194	T=0.6806
gnomAD - Genomes	Other	Sub	2154	C=0.6263	T=0.3737
14KJPN	JAPANESE	Study-wide	28256	C=0.36672	T=0.63328
Allele Frequency Aggregator	Total	Global	22822	C=0.63544	G=0.00000, T=0.36456
Allele Frequency Aggregator	European	Sub	18362	C=0.61872	G=0.00000, T=0.38128
Allele Frequency Aggregator	African	Sub	2760	C=0.7714	G=0.0000, T=0.2286
Allele Frequency Aggregator	Other	Sub	734	C=0.612	G=0.000, T=0.388
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.605	G=0.000, T=0.395
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.699	G=0.000, T=0.301
Allele Frequency Aggregator	Asian	Sub	112	C=0.357	G=0.000, T=0.643
Allele Frequency Aggregator	South Asian	Sub	98	C=0.53	G=0.00, T=0.47
8.3KJPN	JAPANESE	Study-wide	16760	C=0.36790	T=0.63210
1000Genomes_30x	Global	Study-wide	6404	C=0.5915	T=0.4085
1000Genomes_30x	African	Sub	1786	C=0.8012	T=0.1988
1000Genomes_30x	Europe	Sub	1266	C=0.5861	T=0.4139
1000Genomes_30x	South Asian	Sub	1202	C=0.4933	T=0.5067
1000Genomes_30x	East Asian	Sub	1170	C=0.3573	T=0.6427
1000Genomes_30x	American	Sub	980	C=0.616	T=0.384
1000Genomes	Global	Study-wide	5008	C=0.5821	T=0.4179
1000Genomes	African	Sub	1322	C=0.8026	T=0.1974
1000Genomes	East Asian	Sub	1008	C=0.3591	T=0.6409
1000Genomes	Europe	Sub	1006	C=0.5835	T=0.4165
1000Genomes	South Asian	Sub	978	C=0.488	T=0.512
1000Genomes	American	Sub	694	C=0.617	T=0.383
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6690	T=0.3310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6085	T=0.3915
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6044	T=0.3956
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.3675	G=0.0000, T=0.6325
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.629	T=0.371
Northern Sweden	ACPOP	Study-wide	600	C=0.652	T=0.348
SGDP_PRJ	Global	Study-wide	356	C=0.354	T=0.646
Qatari	Global	Study-wide	216	C=0.685	T=0.315
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	T=0.33
Siberian	Global	Study-wide	34	C=0.38	T=0.62

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.973693C>G
GRCh38.p14 chr 1	NC_000001.11:g.973693C>T
GRCh37.p13 chr 1	NC_000001.10:g.909073C>G
GRCh37.p13 chr 1	NC_000001.10:g.909073C>T

Gene: PLEKHN1, pleckstrin homology domain containing N1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLEKHN1 transcript variant 2	NM_001160184.2:c.1329+53C… NM_001160184.2:c.1329+53C>G	N/A	Intron Variant
PLEKHN1 transcript variant 3	NM_001367552.1:c.1470+53C… NM_001367552.1:c.1470+53C>G	N/A	Intron Variant
PLEKHN1 transcript variant 1	NM_032129.3:c.1434+53C>G	N/A	Intron Variant
PLEKHN1 transcript variant X1	XM_011542248.3:c.1590+53C… XM_011542248.3:c.1590+53C>G	N/A	Intron Variant
PLEKHN1 transcript variant X3	XM_017002474.2:c.1449+53C… XM_017002474.2:c.1449+53C>G	N/A	Intron Variant
PLEKHN1 transcript variant X1	XM_017002475.2:c.1450-140… XM_017002475.2:c.1450-140C>G	N/A	Intron Variant
PLEKHN1 transcript variant X2	XM_047431794.1:c.1330-140… XM_047431794.1:c.1330-140C>G	N/A	Intron Variant
PLEKHN1 transcript variant X5	XM_017002478.3:c.	N/A	Genic Downstream Transcript Variant
PLEKHN1 transcript variant X6	XM_017002479.2:c.	N/A	Genic Downstream Transcript Variant
PLEKHN1 transcript variant X4	XM_047431795.1:c.	N/A	Genic Downstream 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	C=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.973693=	NC_000001.11:g.973693C>G	NC_000001.11:g.973693C>T
GRCh37.p13 chr 1	NC_000001.10:g.909073=	NC_000001.10:g.909073C>G	NC_000001.10:g.909073C>T
PLEKHN1 transcript variant 2	NM_001160184.1:c.1329+53=	NM_001160184.1:c.1329+53C>G	NM_001160184.1:c.1329+53C>T
PLEKHN1 transcript variant 2	NM_001160184.2:c.1329+53=	NM_001160184.2:c.1329+53C>G	NM_001160184.2:c.1329+53C>T
PLEKHN1 transcript variant 3	NM_001367552.1:c.1470+53=	NM_001367552.1:c.1470+53C>G	NM_001367552.1:c.1470+53C>T
PLEKHN1 transcript variant 1	NM_032129.2:c.1434+53=	NM_032129.2:c.1434+53C>G	NM_032129.2:c.1434+53C>T
PLEKHN1 transcript variant 1	NM_032129.3:c.1434+53=	NM_032129.3:c.1434+53C>G	NM_032129.3:c.1434+53C>T
PLEKHN1 transcript variant X1	XM_005244809.1:c.1590+53=	XM_005244809.1:c.1590+53C>G	XM_005244809.1:c.1590+53C>T
PLEKHN1 transcript variant X1	XM_011542248.3:c.1590+53=	XM_011542248.3:c.1590+53C>G	XM_011542248.3:c.1590+53C>T
PLEKHN1 transcript variant X3	XM_017002474.2:c.1449+53=	XM_017002474.2:c.1449+53C>G	XM_017002474.2:c.1449+53C>T
PLEKHN1 transcript variant X1	XM_017002475.2:c.1450-140=	XM_017002475.2:c.1450-140C>G	XM_017002475.2:c.1450-140C>T
PLEKHN1 transcript variant X2	XM_047431794.1:c.1330-140=	XM_047431794.1:c.1330-140C>G	XM_047431794.1:c.1330-140C>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#.

87 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1296869	Oct 10, 2002 (108)
2	SSAHASNP	ss22882339	Apr 05, 2004 (121)
3	ABI	ss41170613	Mar 14, 2006 (126)
4	SI_EXO	ss52078590	Oct 16, 2006 (127)
5	HGSV	ss83907803	Dec 14, 2007 (130)
6	BCMHGSC_JDW	ss87157107	Mar 23, 2008 (129)
7	HUMANGENOME_JCVI	ss99179628	Feb 03, 2009 (130)
8	BGI	ss102713467	Dec 01, 2009 (131)
9	1000GENOMES	ss109939141	Jan 24, 2009 (130)
10	ENSEMBL	ss131823153	Dec 01, 2009 (131)
11	ENSEMBL	ss137753738	Dec 01, 2009 (131)
12	GMI	ss154525650	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162981818	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss165981473	Jul 04, 2010 (132)
15	BUSHMAN	ss197886972	Jul 04, 2010 (132)
16	1000GENOMES	ss218191215	Jul 14, 2010 (132)
17	1000GENOMES	ss230395986	Jul 14, 2010 (132)
18	1000GENOMES	ss238115593	Jul 15, 2010 (132)
19	BL	ss252865535	May 09, 2011 (134)
20	GMI	ss275681896	May 04, 2012 (137)
21	PJP	ss290494073	May 09, 2011 (134)
22	ILLUMINA	ss482428651	May 04, 2012 (137)
23	ILLUMINA	ss483257560	May 04, 2012 (137)
24	TISHKOFF	ss553711844	Apr 25, 2013 (138)
25	SSMP	ss647517401	Apr 25, 2013 (138)
26	ILLUMINA	ss782072274	Sep 08, 2015 (146)
27	EVA-GONL	ss974770666	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1067612960	Aug 21, 2014 (142)
29	1000GENOMES	ss1289344763	Aug 21, 2014 (142)
30	DDI	ss1425685354	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1573851531	Apr 01, 2015 (144)
32	EVA_DECODE	ss1584130611	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1599380258	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1642374291	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1793713713	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1917962187	Feb 12, 2016 (147)
37	JJLAB	ss2019499085	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2147485624	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2159374766	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2624265095	Nov 08, 2017 (151)
41	ILLUMINA	ss2632465593	Nov 08, 2017 (151)
42	GRF	ss2697376578	Nov 08, 2017 (151)
43	GNOMAD	ss2750655497	Nov 08, 2017 (151)
44	SWEGEN	ss2986151894	Nov 08, 2017 (151)
45	ILLUMINA	ss3021043396	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023513956	Nov 08, 2017 (151)
47	CSHL	ss3343273435	Nov 08, 2017 (151)
48	ILLUMINA	ss3641566241	Oct 11, 2018 (152)
49	OMUKHERJEE_ADBS	ss3646218812	Oct 11, 2018 (152)
50	URBANLAB	ss3646581518	Oct 11, 2018 (152)
51	ILLUMINA	ss3651365449	Oct 11, 2018 (152)
52	EGCUT_WGS	ss3654263151	Jul 12, 2019 (153)
53	EVA_DECODE	ss3685994781	Jul 12, 2019 (153)
54	ACPOP	ss3726717449	Jul 12, 2019 (153)
55	EVA	ss3745722565	Jul 12, 2019 (153)
56	PACBIO	ss3783302669	Jul 12, 2019 (153)
57	PACBIO	ss3788980331	Jul 12, 2019 (153)
58	PACBIO	ss3793852887	Jul 12, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3798745264	Jul 12, 2019 (153)
60	EVA	ss3825549007	Apr 25, 2020 (154)
61	EVA	ss3825982009	Apr 25, 2020 (154)
62	EVA	ss3836378701	Apr 25, 2020 (154)
63	EVA	ss3841782726	Apr 25, 2020 (154)
64	SGDP_PRJ	ss3847999556	Apr 25, 2020 (154)
65	KRGDB	ss3892841565	Apr 25, 2020 (154)
66	FSA-LAB	ss3983910426	Apr 25, 2021 (155)
67	FSA-LAB	ss3983910427	Apr 25, 2021 (155)
68	EVA	ss3986090826	Apr 25, 2021 (155)
69	TOPMED	ss4436476294	Apr 25, 2021 (155)
70	TOMMO_GENOMICS	ss5142059484	Apr 25, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5240868405	Oct 12, 2022 (156)
72	EVA	ss5316191734	Oct 12, 2022 (156)
73	HUGCELL_USP	ss5442115995	Oct 12, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5512495108	Oct 12, 2022 (156)
75	EVA	ss5623912089	Oct 12, 2022 (156)
76	EVA	ss5623985538	Oct 12, 2022 (156)
77	SANFORD_IMAGENETICS	ss5624752457	Oct 12, 2022 (156)
78	TOMMO_GENOMICS	ss5666201202	Oct 12, 2022 (156)
79	EVA	ss5800076376	Oct 12, 2022 (156)
80	YY_MCH	ss5800245097	Oct 12, 2022 (156)
81	EVA	ss5831420535	Oct 12, 2022 (156)
82	EVA	ss5848243220	Oct 12, 2022 (156)
83	EVA	ss5848749305	Oct 12, 2022 (156)
84	EVA	ss5906709565	Oct 12, 2022 (156)
85	EVA	ss5936507357	Oct 12, 2022 (156)
86	EVA	ss5936585079	Oct 12, 2022 (156)
87	EVA	ss5979926211	Oct 12, 2022 (156)
88	1000Genomes	NC_000001.10 - 909073	Oct 11, 2018 (152)
89	1000Genomes_30x	NC_000001.11 - 973693	Oct 12, 2022 (156)
90	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 909073	Oct 11, 2018 (152)
91	Genetic variation in the Estonian population	NC_000001.10 - 909073	Oct 11, 2018 (152)
92	The Danish reference pan genome	NC_000001.10 - 909073	Apr 25, 2020 (154)
93	gnomAD - Genomes	NC_000001.11 - 973693	Apr 25, 2021 (155)
94	Genome of the Netherlands Release 5	NC_000001.10 - 909073	Apr 25, 2020 (154)
95	KOREAN population from KRGDB	NC_000001.10 - 909073	Apr 25, 2020 (154)
96	Northern Sweden	NC_000001.10 - 909073	Jul 12, 2019 (153)
97	Qatari	NC_000001.10 - 909073	Apr 25, 2020 (154)
98	SGDP_PRJ	NC_000001.10 - 909073	Apr 25, 2020 (154)
99	Siberian	NC_000001.10 - 909073	Apr 25, 2020 (154)
100	8.3KJPN	NC_000001.10 - 909073	Apr 25, 2021 (155)
101	14KJPN	NC_000001.11 - 973693	Oct 12, 2022 (156)
102	TopMed	NC_000001.11 - 973693	Apr 25, 2021 (155)
103	UK 10K study - Twins	NC_000001.10 - 909073	Oct 11, 2018 (152)
104	ALFA	NC_000001.11 - 973693	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)
rs56858257	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
18959, ss3892841565	NC_000001.10:909072:C:G	NC_000001.11:973692:C:G	(self)
12928527362	NC_000001.11:973692:C:G	NC_000001.11:973692:C:G	(self)
ss83907803	NC_000001.8:949139:C:T	NC_000001.11:973692:C:T	(self)
ss87157107, ss109939141, ss162981818, ss165981473, ss197886972, ss252865535, ss275681896, ss290494073, ss482428651, ss1584130611	NC_000001.9:898935:C:T	NC_000001.11:973692:C:T	(self)
9710, 2427, 1399, 1358765, 1412, 18959, 2314, 4117, 16536, 1978, 28791, 2427, ss218191215, ss230395986, ss238115593, ss483257560, ss553711844, ss647517401, ss782072274, ss974770666, ss1067612960, ss1289344763, ss1425685354, ss1573851531, ss1599380258, ss1642374291, ss1793713713, ss1917962187, ss2019499085, ss2147485624, ss2624265095, ss2632465593, ss2697376578, ss2750655497, ss2986151894, ss3021043396, ss3343273435, ss3641566241, ss3646218812, ss3651365449, ss3654263151, ss3726717449, ss3745722565, ss3783302669, ss3788980331, ss3793852887, ss3825549007, ss3825982009, ss3836378701, ss3847999556, ss3892841565, ss3983910426, ss3983910427, ss3986090826, ss5142059484, ss5316191734, ss5623912089, ss5623985538, ss5624752457, ss5800076376, ss5831420535, ss5848243220, ss5936507357, ss5936585079, ss5979926211	NC_000001.10:909072:C:T	NC_000001.11:973692:C:T	(self)
21043, 102201, 38306, 82629, 12928527362, ss2159374766, ss3023513956, ss3646581518, ss3685994781, ss3798745264, ss3841782726, ss4436476294, ss5240868405, ss5442115995, ss5512495108, ss5666201202, ss5800245097, ss5848749305, ss5906709565	NC_000001.11:973692:C:T	NC_000001.11:973692:C:T	(self)
ss1296869, ss22882339, ss41170613, ss99179628, ss102713467, ss131823153, ss137753738, ss154525650	NT_004350.19:387704:C:T	NC_000001.11:973692:C:T	(self)
ss52078590	NT_077913.3:387908:C:T	NC_000001.11:973692:C: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 rs3892467

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

rs3892467