Name: rs58212655
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.

rs58212655

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:767238 (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: T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.104620 (27692/264690, TOPMED)
G=0.08925 (2522/28258, 14KJPN)
G=0.04691 (789/16820, ALFA) (+ 13 more)
G=0.09016 (1511/16760, 8.3KJPN)
G=0.1168 (585/5008, 1000G)
G=0.1252 (561/4480, Estonian)
G=0.0719 (277/3854, ALSPAC)
G=0.0698 (259/3708, TWINSUK)
G=0.0819 (240/2930, KOREAN)
G=0.077 (77/998, GoNL)
G=0.070 (42/600, NorthernSweden)
G=0.069 (15/216, Qatari)
T=0.394 (56/142, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
T=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PCGF3-AS1 : Intron Variant
PCGF3 : 3 Prime UTR Variant
LOC124900163 : 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	16820	T=0.95309	C=0.00000, G=0.04691
European	Sub	13042	T=0.94518	C=0.00000, G=0.05482
African	Sub	2142	T=0.9897	C=0.0000, G=0.0103
African Others	Sub	78	T=0.99	C=0.00, G=0.01
African American	Sub	2064	T=0.9898	C=0.0000, G=0.0102
Asian	Sub	104	T=0.990	C=0.000, G=0.010
East Asian	Sub	82	T=1.00	C=0.00, G=0.00
Other Asian	Sub	22	T=0.95	C=0.00, G=0.05
Latin American 1	Sub	124	T=1.000	C=0.000, G=0.000
Latin American 2	Sub	486	T=0.998	C=0.000, G=0.002
South Asian	Sub	76	T=0.99	C=0.00, G=0.01
Other	Sub	846	T=0.942	C=0.000, G=0.058

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	T=0.895380	G=0.104620
14KJPN	JAPANESE	Study-wide	28258	T=0.91075	G=0.08925
Allele Frequency Aggregator	Total	Global	16820	T=0.95309	C=0.00000, G=0.04691
Allele Frequency Aggregator	European	Sub	13042	T=0.94518	C=0.00000, G=0.05482
Allele Frequency Aggregator	African	Sub	2142	T=0.9897	C=0.0000, G=0.0103
Allele Frequency Aggregator	Other	Sub	846	T=0.942	C=0.000, G=0.058
Allele Frequency Aggregator	Latin American 2	Sub	486	T=0.998	C=0.000, G=0.002
Allele Frequency Aggregator	Latin American 1	Sub	124	T=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	104	T=0.990	C=0.000, G=0.010
Allele Frequency Aggregator	South Asian	Sub	76	T=0.99	C=0.00, G=0.01
8.3KJPN	JAPANESE	Study-wide	16760	T=0.90984	G=0.09016
1000Genomes	Global	Study-wide	5008	T=0.8832	G=0.1168
1000Genomes	African	Sub	1322	T=0.8306	G=0.1694
1000Genomes	East Asian	Sub	1008	T=0.9385	G=0.0615
1000Genomes	Europe	Sub	1006	T=0.9235	G=0.0765
1000Genomes	South Asian	Sub	978	T=0.842	G=0.158
1000Genomes	American	Sub	694	T=0.903	G=0.097
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8748	G=0.1252
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9281	G=0.0719
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9302	G=0.0698
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.9181	G=0.0819
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.923	G=0.077
Northern Sweden	ACPOP	Study-wide	600	T=0.930	G=0.070
Qatari	Global	Study-wide	216	T=0.931	G=0.069
SGDP_PRJ	Global	Study-wide	142	T=0.394	C=0.007, G=0.599
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	G=0.10
Siberian	Global	Study-wide	16	T=0.50	G=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.767238T>C
GRCh38.p14 chr 4	NC_000004.12:g.767238T>G
GRCh37.p13 chr 4	NC_000004.11:g.761026T>C
GRCh37.p13 chr 4	NC_000004.11:g.761026T>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
PCGF3 transcript variant 7	NM_001395249.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 6	NM_001395248.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 1	NM_001317836.3:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 5	NM_001395247.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 4	NM_001395246.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 3	NM_001395245.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 2	NM_006315.7:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 9	NM_001395251.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant 8	NM_001395250.1:c.*1159=	N/A	3 Prime UTR Variant
PCGF3 transcript variant X1	XM_047449500.1:c.*1159=	N/A	3 Prime UTR 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.	N/A	Intron 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.-2792-43… XM_047416472.1:c.-2792-4399A>G	N/A	Intron Variant
LOC124900163 transcript variant X3	XM_047416474.1:c.-2693-44… XM_047416474.1:c.-2693-4498A>G	N/A	Intron Variant
LOC124900163 transcript variant X2	XM_047416473.1: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	T=	C	G
GRCh38.p14 chr 4	NC_000004.12:g.767238=	NC_000004.12:g.767238T>C	NC_000004.12:g.767238T>G
GRCh37.p13 chr 4	NC_000004.11:g.761026=	NC_000004.11:g.761026T>C	NC_000004.11:g.761026T>G
PCGF3 transcript variant 2	NM_006315.7:c.*1159=	NM_006315.7:c.*1159T>C	NM_006315.7:c.*1159T>G
PCGF3 transcript variant 2	NM_006315.6:c.*1159=	NM_006315.6:c.*1159T>C	NM_006315.6:c.*1159T>G
PCGF3 transcript variant 2	NM_006315.5:c.*1159=	NM_006315.5:c.*1159T>C	NM_006315.5:c.*1159T>G
PCGF3 transcript	NM_006315.4:c.*1159=	NM_006315.4:c.*1159T>C	NM_006315.4:c.*1159T>G
PCGF3 transcript variant 1	NM_001317836.3:c.*1159=	NM_001317836.3:c.*1159T>C	NM_001317836.3:c.*1159T>G
PCGF3 transcript variant 1	NM_001317836.2:c.*1159=	NM_001317836.2:c.*1159T>C	NM_001317836.2:c.*1159T>G
PCGF3 transcript variant 1	NM_001317836.1:c.*1159=	NM_001317836.1:c.*1159T>C	NM_001317836.1:c.*1159T>G
PCGF3 transcript variant X1	XM_047449500.1:c.*1159=	XM_047449500.1:c.*1159T>C	XM_047449500.1:c.*1159T>G
PCGF3 transcript variant 8	NM_001395250.1:c.*1159=	NM_001395250.1:c.*1159T>C	NM_001395250.1:c.*1159T>G
PCGF3 transcript variant 3	NM_001395245.1:c.*1159=	NM_001395245.1:c.*1159T>C	NM_001395245.1:c.*1159T>G
PCGF3 transcript variant 9	NM_001395251.1:c.*1159=	NM_001395251.1:c.*1159T>C	NM_001395251.1:c.*1159T>G
PCGF3 transcript variant 4	NM_001395246.1:c.*1159=	NM_001395246.1:c.*1159T>C	NM_001395246.1:c.*1159T>G
PCGF3 transcript variant 5	NM_001395247.1:c.*1159=	NM_001395247.1:c.*1159T>C	NM_001395247.1:c.*1159T>G
PCGF3 transcript variant 6	NM_001395248.1:c.*1159=	NM_001395248.1:c.*1159T>C	NM_001395248.1:c.*1159T>G
PCGF3 transcript variant 7	NM_001395249.1:c.*1159=	NM_001395249.1:c.*1159T>C	NM_001395249.1:c.*1159T>G
LOC124900163 transcript variant X1	XM_047416472.1:c.-2792-4399=	XM_047416472.1:c.-2792-4399A>G	XM_047416472.1:c.-2792-4399A>C
LOC124900163 transcript variant X3	XM_047416474.1:c.-2693-4498=	XM_047416474.1:c.-2693-4498A>G	XM_047416474.1:c.-2693-4498A>C

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#.

55 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss84829937	Dec 15, 2007 (129)
2	ILLUMINA-UK	ss116834987	Feb 14, 2009 (130)
3	COMPLETE_GENOMICS	ss162988358	Jul 04, 2010 (132)
4	ILLUMINA	ss169030411	Jul 04, 2010 (132)
5	1000GENOMES	ss211342469	Jul 14, 2010 (132)
6	1000GENOMES	ss220689712	Jul 14, 2010 (132)
7	1000GENOMES	ss232222356	Jul 14, 2010 (132)
8	1000GENOMES	ss239551785	Jul 15, 2010 (132)
9	GMI	ss277536563	May 04, 2012 (137)
10	ILLUMINA	ss535761166	Sep 08, 2015 (146)
11	TISHKOFF	ss557249105	Apr 25, 2013 (138)
12	SSMP	ss651001532	Apr 25, 2013 (138)
13	EVA-GONL	ss979664938	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1071210433	Aug 21, 2014 (142)
15	1000GENOMES	ss1308056530	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1580377510	Apr 01, 2015 (144)
17	EVA_DECODE	ss1589161881	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1609220922	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1652214955	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1800779770	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1922894946	Feb 12, 2016 (147)
22	GENOMED	ss1969636140	Jul 19, 2016 (147)
23	JJLAB	ss2022021631	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2150126678	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2259757795	Dec 20, 2016 (150)
26	GRF	ss2705561244	Nov 08, 2017 (151)
27	GNOMAD	ss2804596405	Nov 08, 2017 (151)
28	SWEGEN	ss2993979400	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3024780451	Nov 08, 2017 (151)
30	CSHL	ss3345494273	Nov 08, 2017 (151)
31	ILLUMINA	ss3628882398	Oct 12, 2018 (152)
32	ILLUMINA	ss3638467161	Oct 12, 2018 (152)
33	OMUKHERJEE_ADBS	ss3646299817	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3661918542	Jul 13, 2019 (153)
35	EVA_DECODE	ss3711219973	Jul 13, 2019 (153)
36	ACPOP	ss3730771219	Jul 13, 2019 (153)
37	EVA	ss3761274237	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3804415305	Jul 13, 2019 (153)
39	EVA	ss3825650951	Apr 25, 2020 (154)
40	EVA	ss3828322254	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3858004427	Apr 25, 2020 (154)
42	KRGDB	ss3904127145	Apr 25, 2020 (154)
43	TOPMED	ss4599917461	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5163777844	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5257713016	Oct 17, 2022 (156)
46	EVA	ss5346319900	Oct 17, 2022 (156)
47	HUGCELL_USP	ss5456672721	Oct 17, 2022 (156)
48	EVA	ss5507365754	Oct 17, 2022 (156)
49	SANFORD_IMAGENETICS	ss5634157802	Oct 17, 2022 (156)
50	TOMMO_GENOMICS	ss5697298578	Oct 17, 2022 (156)
51	YY_MCH	ss5804670214	Oct 17, 2022 (156)
52	EVA	ss5843417030	Oct 17, 2022 (156)
53	EVA	ss5854042966	Oct 17, 2022 (156)
54	EVA	ss5861784299	Oct 17, 2022 (156)
55	EVA	ss5962533918	Oct 17, 2022 (156)
56	1000Genomes	NC_000004.11 - 761026	Oct 12, 2018 (152)
57	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 761026	Oct 12, 2018 (152)
58	Genetic variation in the Estonian population	NC_000004.11 - 761026	Oct 12, 2018 (152)
59	The Danish reference pan genome	NC_000004.11 - 761026	Apr 25, 2020 (154)
60	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137681144 (NC_000004.12:767237:T:C 11/140102) Row 137681145 (NC_000004.12:767237:T:G 14953/140084)	-	Apr 26, 2021 (155)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137681144 (NC_000004.12:767237:T:C 11/140102) Row 137681145 (NC_000004.12:767237:T:G 14953/140084)	-	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000004.11 - 761026	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000004.11 - 761026	Apr 25, 2020 (154)
64	Northern Sweden	NC_000004.11 - 761026	Jul 13, 2019 (153)
65	Qatari	NC_000004.11 - 761026	Apr 25, 2020 (154)
66	SGDP_PRJ	NC_000004.11 - 761026	Apr 25, 2020 (154)
67	Siberian	NC_000004.11 - 761026	Apr 25, 2020 (154)
68	8.3KJPN	NC_000004.11 - 761026	Apr 26, 2021 (155)
69	14KJPN	NC_000004.12 - 767238	Oct 17, 2022 (156)
70	TopMed	NC_000004.12 - 767238	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000004.11 - 761026	Oct 12, 2018 (152)
72	ALFA	NC_000004.12 - 767238	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
10021407, ss557249105, ss1800779770, ss2804596405, ss3858004427	NC_000004.11:761025:T:C	NC_000004.12:767237:T:C	(self)
12391489782, ss2259757795	NC_000004.12:767237:T:C	NC_000004.12:767237:T:C	(self)
ss84829937	NC_000004.9:750855:T:G	NC_000004.12:767237:T:G	(self)
ss116834987, ss162988358, ss211342469, ss277536563, ss1589161881	NC_000004.10:751025:T:G	NC_000004.12:767237:T:G	(self)
19393474, 10811639, 7656790, 6542449, 4752360, 11304539, 4056084, 4936876, 10021407, 2643032, 21747151, 10811639, ss220689712, ss232222356, ss239551785, ss535761166, ss557249105, ss651001532, ss979664938, ss1071210433, ss1308056530, ss1580377510, ss1609220922, ss1652214955, ss1922894946, ss1969636140, ss2022021631, ss2150126678, ss2705561244, ss2804596405, ss2993979400, ss3345494273, ss3628882398, ss3638467161, ss3646299817, ss3661918542, ss3730771219, ss3761274237, ss3825650951, ss3828322254, ss3858004427, ss3904127145, ss5163777844, ss5346319900, ss5507365754, ss5634157802, ss5843417030, ss5962533918	NC_000004.11:761025:T:G	NC_000004.12:767237:T:G	(self)
31135682, 437295017, 12391489782, ss2259757795, ss3024780451, ss3711219973, ss3804415305, ss4599917461, ss5257713016, ss5456672721, ss5697298578, ss5804670214, ss5854042966, ss5861784299	NC_000004.12:767237:T:G	NC_000004.12:767237:T:G	(self)
ss169030411	NT_037622.5:751025:T:G	NC_000004.12:767237:T: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 rs58212655

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs58212655