Name: rs73222811
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.

rs73222811

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:762481 (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=0.17648 (4987/28258, 14KJPN)
T=0.02173 (387/17808, ALFA)
T=0.17518 (2936/16760, 8.3KJPN) (+ 15 more)
T=0.0532 (341/6404, 1000G_30x)
T=0.0567 (284/5008, 1000G)
T=0.0397 (178/4480, Estonian)
T=0.0646 (249/3854, ALSPAC)
T=0.0520 (193/3708, TWINSUK)
T=0.1457 (427/2930, KOREAN)
T=0.1343 (246/1832, Korea1K)
T=0.045 (45/998, GoNL)
T=0.063 (38/600, NorthernSweden)
T=0.079 (17/216, Qatari)
T=0.065 (14/214, Vietnamese)
C=0.46 (34/74, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.50 (8/16, Siberian)
T=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PCGF3-AS1 : Non Coding Transcript Variant
PCGF3 : Intron Variant
LOC124900163 : 5 Prime UTR 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	17808	C=0.97827	G=0.00000, T=0.02173
European	Sub	13438	C=0.97299	G=0.00000, T=0.02701
African	Sub	2868	C=0.9979	G=0.0000, T=0.0021
African Others	Sub	112	C=1.000	G=0.000, T=0.000
African American	Sub	2756	C=0.9978	G=0.0000, T=0.0022
Asian	Sub	94	C=1.00	G=0.00, T=0.00
East Asian	Sub	68	C=1.00	G=0.00, T=0.00
Other Asian	Sub	26	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	124	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	552	C=1.000	G=0.000, T=0.000
South Asian	Sub	90	C=1.00	G=0.00, T=0.00
Other	Sub	642	C=0.972	G=0.000, T=0.028

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
14KJPN	JAPANESE	Study-wide	28258	C=0.82352	T=0.17648
Allele Frequency Aggregator	Total	Global	17808	C=0.97827	G=0.00000, T=0.02173
Allele Frequency Aggregator	European	Sub	13438	C=0.97299	G=0.00000, T=0.02701
Allele Frequency Aggregator	African	Sub	2868	C=0.9979	G=0.0000, T=0.0021
Allele Frequency Aggregator	Other	Sub	642	C=0.972	G=0.000, T=0.028
Allele Frequency Aggregator	Latin American 2	Sub	552	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	124	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	94	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	90	C=1.00	G=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.82482	T=0.17518
1000Genomes_30x	Global	Study-wide	6404	C=0.9468	T=0.0532
1000Genomes_30x	African	Sub	1786	C=0.9871	T=0.0129
1000Genomes_30x	Europe	Sub	1266	C=0.9423	T=0.0577
1000Genomes_30x	South Asian	Sub	1202	C=0.9526	T=0.0474
1000Genomes_30x	East Asian	Sub	1170	C=0.8812	T=0.1188
1000Genomes_30x	American	Sub	980	C=0.950	T=0.050
1000Genomes	Global	Study-wide	5008	C=0.9433	T=0.0567
1000Genomes	African	Sub	1322	C=0.9879	T=0.0121
1000Genomes	East Asian	Sub	1008	C=0.8750	T=0.1250
1000Genomes	Europe	Sub	1006	C=0.9423	T=0.0577
1000Genomes	South Asian	Sub	978	C=0.949	T=0.051
1000Genomes	American	Sub	694	C=0.951	T=0.049
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9603	T=0.0397
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9354	T=0.0646
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9480	T=0.0520
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8543	T=0.1457
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8657	T=0.1343
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.955	T=0.045
Northern Sweden	ACPOP	Study-wide	600	C=0.937	T=0.063
Qatari	Global	Study-wide	216	C=0.921	T=0.079
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.935	T=0.065
SGDP_PRJ	Global	Study-wide	74	C=0.46	T=0.54
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	16	C=0.50	T=0.50

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 4	NC_000004.12:g.762481C>G
GRCh38.p14 chr 4	NC_000004.12:g.762481C>T
GRCh37.p13 chr 4	NC_000004.11:g.756269C>G
GRCh37.p13 chr 4	NC_000004.11:g.756269C>T

Gene: PCGF3, polycomb group ring finger 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PCGF3 transcript variant 1	NM_001317836.3:c.600+1065… NM_001317836.3:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 3	NM_001395245.1:c.600+1065… NM_001395245.1:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 4	NM_001395246.1:c.600+1065… NM_001395246.1:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 5	NM_001395247.1:c.600+1065… NM_001395247.1:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 6	NM_001395248.1:c.600+1065… NM_001395248.1:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 7	NM_001395249.1:c.600+1065… NM_001395249.1:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 8	NM_001395250.1:c.498+1065… NM_001395250.1:c.498+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 9	NM_001395251.1:c.498+1065… NM_001395251.1:c.498+1065C>G	N/A	Intron Variant
PCGF3 transcript variant 2	NM_006315.7:c.600+1065C>G	N/A	Intron Variant
PCGF3 transcript variant X1	XM_047449500.1:c.498+1065… XM_047449500.1:c.498+1065C>G	N/A	Intron Variant

Gene: PCGF3-AS1, PCGF3 antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PCGF3-AS1 transcript variant 3	NR_171661.1:n.2343G>C	N/A	Non Coding Transcript Variant
PCGF3-AS1 transcript variant 3	NR_171661.1:n.2343G>A	N/A	Non Coding Transcript Variant
PCGF3-AS1 transcript variant 1	NR_036511.1:n.	N/A	Genic Downstream Transcript Variant
PCGF3-AS1 transcript variant 2	NR_036512.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC124900163, uncharacterized LOC124900163 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124900163 transcript variant X1	XM_047416472.1:c.-2434=	N/A	5 Prime UTR Variant
LOC124900163 transcript variant X2	XM_047416473.1:c.-2434=	N/A	5 Prime UTR Variant
LOC124900163 transcript variant X3	XM_047416474.1:c.-2434=	N/A	5 Prime UTR 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 4	NC_000004.12:g.762481=	NC_000004.12:g.762481C>G	NC_000004.12:g.762481C>T
GRCh37.p13 chr 4	NC_000004.11:g.756269=	NC_000004.11:g.756269C>G	NC_000004.11:g.756269C>T
LOC124900163 transcript variant X2	XM_047416473.1:c.-2434=	XM_047416473.1:c.-2434G>C	XM_047416473.1:c.-2434G>A
LOC124900163 transcript variant X1	XM_047416472.1:c.-2434=	XM_047416472.1:c.-2434G>C	XM_047416472.1:c.-2434G>A
LOC124900163 transcript variant X3	XM_047416474.1:c.-2434=	XM_047416474.1:c.-2434G>C	XM_047416474.1:c.-2434G>A
PCGF3-AS1 transcript variant 3	NR_171661.1:n.2343=	NR_171661.1:n.2343G>C	NR_171661.1:n.2343G>A
PCGF3 transcript variant 1	NM_001317836.3:c.600+1065=	NM_001317836.3:c.600+1065C>G	NM_001317836.3:c.600+1065C>T
PCGF3 transcript variant 3	NM_001395245.1:c.600+1065=	NM_001395245.1:c.600+1065C>G	NM_001395245.1:c.600+1065C>T
PCGF3 transcript variant 4	NM_001395246.1:c.600+1065=	NM_001395246.1:c.600+1065C>G	NM_001395246.1:c.600+1065C>T
PCGF3 transcript variant 5	NM_001395247.1:c.600+1065=	NM_001395247.1:c.600+1065C>G	NM_001395247.1:c.600+1065C>T
PCGF3 transcript variant 6	NM_001395248.1:c.600+1065=	NM_001395248.1:c.600+1065C>G	NM_001395248.1:c.600+1065C>T
PCGF3 transcript variant 7	NM_001395249.1:c.600+1065=	NM_001395249.1:c.600+1065C>G	NM_001395249.1:c.600+1065C>T
PCGF3 transcript variant 8	NM_001395250.1:c.498+1065=	NM_001395250.1:c.498+1065C>G	NM_001395250.1:c.498+1065C>T
PCGF3 transcript variant 9	NM_001395251.1:c.498+1065=	NM_001395251.1:c.498+1065C>G	NM_001395251.1:c.498+1065C>T
PCGF3 transcript	NM_006315.4:c.600+1065=	NM_006315.4:c.600+1065C>G	NM_006315.4:c.600+1065C>T
PCGF3 transcript variant 2	NM_006315.7:c.600+1065=	NM_006315.7:c.600+1065C>G	NM_006315.7:c.600+1065C>T
PCGF3 transcript variant X1	XM_005272250.1:c.600+1065=	XM_005272250.1:c.600+1065C>G	XM_005272250.1:c.600+1065C>T
PCGF3 transcript variant X2	XM_005272251.1:c.600+1065=	XM_005272251.1:c.600+1065C>G	XM_005272251.1:c.600+1065C>T
PCGF3 transcript variant X3	XM_005272253.1:c.498+1065=	XM_005272253.1:c.498+1065C>G	XM_005272253.1:c.498+1065C>T
PCGF3 transcript variant X4	XM_005272254.1:c.498+1065=	XM_005272254.1:c.498+1065C>G	XM_005272254.1:c.498+1065C>T
PCGF3 transcript variant X6	XM_005272255.1:c.498+1065=	XM_005272255.1:c.498+1065C>G	XM_005272255.1:c.498+1065C>T
PCGF3 transcript variant X7	XM_005272256.1:c.498+1065=	XM_005272256.1:c.498+1065C>G	XM_005272256.1:c.498+1065C>T
PCGF3 transcript variant X1	XM_047449500.1:c.498+1065=	XM_047449500.1:c.498+1065C>G	XM_047449500.1:c.498+1065C>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#.

48 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss112841764	Feb 14, 2009 (130)
2	BCM-HGSC-SUB	ss206655828	Jul 04, 2010 (132)
3	1000GENOMES	ss232222317	Jul 14, 2010 (132)
4	1000GENOMES	ss239551749	Jul 15, 2010 (132)
5	SSMP	ss651001476	Apr 25, 2013 (138)
6	EVA-GONL	ss979664841	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1071210384	Aug 21, 2014 (142)
8	1000GENOMES	ss1308056215	Aug 21, 2014 (142)
9	DDI	ss1429737064	Apr 01, 2015 (144)
10	EVA_GENOME_DK	ss1580377473	Apr 01, 2015 (144)
11	EVA_DECODE	ss1589161795	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1609220742	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1652214775	Apr 01, 2015 (144)
14	HAMMER_LAB	ss1800779718	Sep 08, 2015 (146)
15	WEILL_CORNELL_DGM	ss1922894870	Feb 12, 2016 (147)
16	JJLAB	ss2022021583	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2150126634	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2259757172	Dec 20, 2016 (150)
19	GRF	ss2705561187	Nov 08, 2017 (151)
20	GNOMAD	ss2804595603	Nov 08, 2017 (151)
21	SWEGEN	ss2993979282	Nov 08, 2017 (151)
22	CSHL	ss3345494231	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3645770911	Oct 12, 2018 (152)
24	EGCUT_WGS	ss3661918405	Jul 13, 2019 (153)
25	EVA_DECODE	ss3711219824	Jul 13, 2019 (153)
26	ACPOP	ss3730771154	Jul 13, 2019 (153)
27	EVA	ss3761274129	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3804415207	Jul 13, 2019 (153)
29	EVA	ss3828322219	Apr 25, 2020 (154)
30	EVA	ss3837592271	Apr 25, 2020 (154)
31	EVA	ss3843025522	Apr 25, 2020 (154)
32	SGDP_PRJ	ss3858004289	Apr 25, 2020 (154)
33	KRGDB	ss3904126989	Apr 25, 2020 (154)
34	KOGIC	ss3953335017	Apr 25, 2020 (154)
35	TOPMED	ss4599915080	Apr 26, 2021 (155)
36	TOPMED	ss4599915081	Apr 26, 2021 (155)
37	TOMMO_GENOMICS	ss5163777484	Apr 26, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5257712730	Oct 17, 2022 (156)
39	EVA	ss5346319425	Oct 17, 2022 (156)
40	HUGCELL_USP	ss5456672535	Oct 17, 2022 (156)
41	EVA	ss5507365718	Oct 17, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5537999113	Oct 17, 2022 (156)
43	SANFORD_IMAGENETICS	ss5634157670	Oct 17, 2022 (156)
44	TOMMO_GENOMICS	ss5697298132	Oct 17, 2022 (156)
45	YY_MCH	ss5804670145	Oct 17, 2022 (156)
46	EVA	ss5843416933	Oct 17, 2022 (156)
47	EVA	ss5861783964	Oct 17, 2022 (156)
48	EVA	ss5962533776	Oct 17, 2022 (156)
49	1000Genomes	NC_000004.11 - 756269	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000004.12 - 762481	Oct 17, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 756269	Oct 12, 2018 (152)
52	Genetic variation in the Estonian population	NC_000004.11 - 756269	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000004.11 - 756269	Apr 25, 2020 (154)
54	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137679224 (NC_000004.12:762480:C:G 1/140240) Row 137679225 (NC_000004.12:762480:C:T 6874/140230)	-	Apr 26, 2021 (155)
55	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137679224 (NC_000004.12:762480:C:G 1/140240) Row 137679225 (NC_000004.12:762480:C:T 6874/140230)	-	Apr 26, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000004.11 - 756269	Apr 25, 2020 (154)
57	KOREAN population from KRGDB	NC_000004.11 - 756269	Apr 25, 2020 (154)
58	Korean Genome Project	NC_000004.12 - 762481	Apr 25, 2020 (154)
59	Northern Sweden	NC_000004.11 - 756269	Jul 13, 2019 (153)
60	Qatari	NC_000004.11 - 756269	Apr 25, 2020 (154)
61	SGDP_PRJ	NC_000004.11 - 756269	Apr 25, 2020 (154)
62	Siberian	NC_000004.11 - 756269	Apr 25, 2020 (154)
63	8.3KJPN	NC_000004.11 - 756269	Apr 26, 2021 (155)
64	14KJPN	NC_000004.12 - 762481	Oct 17, 2022 (156)
65	TopMed Submission ignored due to conflicting rows: Row 437292636 (NC_000004.12:762480:C:G 4/264690) Row 437292637 (NC_000004.12:762480:C:T 13533/264690)	-	Apr 26, 2021 (155)
66	TopMed Submission ignored due to conflicting rows: Row 437292636 (NC_000004.12:762480:C:G 4/264690) Row 437292637 (NC_000004.12:762480:C:T 13533/264690)	-	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000004.11 - 756269	Oct 12, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000004.11 - 756269	Jul 13, 2019 (153)
69	ALFA	NC_000004.12 - 762481	Apr 26, 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
4012945646, ss4599915080	NC_000004.12:762480:C:G	NC_000004.12:762480:C:G	(self)
ss112841764, ss206655828, ss1589161795	NC_000004.10:746268:C:T	NC_000004.12:762480:C:T	(self)
19393139, 10811446, 7656653, 6542412, 4752263, 11304383, 4056019, 4936800, 10021269, 2642988, 21746791, 10811446, 2364060, ss232222317, ss239551749, ss651001476, ss979664841, ss1071210384, ss1308056215, ss1429737064, ss1580377473, ss1609220742, ss1652214775, ss1800779718, ss1922894870, ss2022021583, ss2150126634, ss2705561187, ss2804595603, ss2993979282, ss3345494231, ss3661918405, ss3730771154, ss3761274129, ss3828322219, ss3837592271, ss3858004289, ss3904126989, ss5163777484, ss5346319425, ss5507365718, ss5634157670, ss5843416933, ss5962533776	NC_000004.11:756268:C:T	NC_000004.12:762480:C:T	(self)
25525048, 9713018, 31135236, 4012945646, ss2259757172, ss3645770911, ss3711219824, ss3804415207, ss3843025522, ss3953335017, ss4599915081, ss5257712730, ss5456672535, ss5537999113, ss5697298132, ss5804670145, ss5861783964	NC_000004.12:762480:C:T	NC_000004.12:762480: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 rs73222811

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

rs73222811