Name: rs4690312
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.

rs4690312

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:775060 (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: G=0.052055 (7297/140178, GnomAD)
G=0.11183 (3160/28258, 14KJPN)
G=0.02118 (371/17520, ALFA) (+ 15 more)
G=0.11331 (1899/16760, 8.3KJPN)
G=0.0981 (628/6404, 1000G_30x)
G=0.0996 (499/5008, 1000G)
G=0.0458 (205/4480, Estonian)
G=0.0667 (257/3854, ALSPAC)
G=0.0720 (267/3708, TWINSUK)
G=0.1598 (467/2922, KOREAN)
G=0.1496 (274/1832, Korea1K)
G=0.069 (69/998, GoNL)
G=0.073 (44/600, NorthernSweden)
G=0.083 (18/216, Qatari)
G=0.236 (51/216, Vietnamese)
C=0.42 (38/90, SGDP_PRJ)
C=0.5 (3/6, Siberian)
G=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PCGF3-AS1 : Intron 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	17520	C=0.97882	G=0.02118, T=0.00000
European	Sub	13268	C=0.97279	G=0.02721, T=0.00000
African	Sub	2876	C=0.9993	G=0.0007, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	2762	C=0.9993	G=0.0007, T=0.0000
Asian	Sub	68	C=1.00	G=0.00, T=0.00
East Asian	Sub	60	C=1.00	G=0.00, T=0.00
Other Asian	Sub	8	C=1.0	G=0.0, T=0.0
Latin American 1	Sub	122	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	484	C=1.000	G=0.000, T=0.000
South Asian	Sub	60	C=0.97	G=0.03, T=0.00
Other	Sub	642	C=0.991	G=0.009, T=0.000

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	140178	C=0.947945	G=0.052055
gnomAD - Genomes	European	Sub	75924	C=0.93899	G=0.06101
gnomAD - Genomes	African	Sub	42010	C=0.98617	G=0.01383
gnomAD - Genomes	American	Sub	13650	C=0.91370	G=0.08630
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9527	G=0.0473
gnomAD - Genomes	East Asian	Sub	3124	C=0.8025	G=0.1975
gnomAD - Genomes	Other	Sub	2150	C=0.9386	G=0.0614
14KJPN	JAPANESE	Study-wide	28258	C=0.88817	G=0.11183
Allele Frequency Aggregator	Total	Global	17520	C=0.97882	G=0.02118, T=0.00000
Allele Frequency Aggregator	European	Sub	13268	C=0.97279	G=0.02721, T=0.00000
Allele Frequency Aggregator	African	Sub	2876	C=0.9993	G=0.0007, T=0.0000
Allele Frequency Aggregator	Other	Sub	642	C=0.991	G=0.009, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	484	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	122	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	68	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	60	C=0.97	G=0.03, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.88669	G=0.11331
1000Genomes_30x	Global	Study-wide	6404	C=0.9019	G=0.0981
1000Genomes_30x	African	Sub	1786	C=0.9955	G=0.0045
1000Genomes_30x	Europe	Sub	1266	C=0.9242	G=0.0758
1000Genomes_30x	South Asian	Sub	1202	C=0.8378	G=0.1622
1000Genomes_30x	East Asian	Sub	1170	C=0.7957	G=0.2043
1000Genomes_30x	American	Sub	980	C=0.908	G=0.092
1000Genomes	Global	Study-wide	5008	C=0.9004	G=0.0996
1000Genomes	African	Sub	1322	C=0.9955	G=0.0045
1000Genomes	East Asian	Sub	1008	C=0.7996	G=0.2004
1000Genomes	Europe	Sub	1006	C=0.9314	G=0.0686
1000Genomes	South Asian	Sub	978	C=0.843	G=0.157
1000Genomes	American	Sub	694	C=0.902	G=0.098
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9542	G=0.0458
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9333	G=0.0667
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9280	G=0.0720
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8402	G=0.1598
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8504	G=0.1496
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.931	G=0.069
Northern Sweden	ACPOP	Study-wide	600	C=0.927	G=0.073
Qatari	Global	Study-wide	216	C=0.917	G=0.083
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.764	G=0.236
SGDP_PRJ	Global	Study-wide	90	C=0.42	G=0.58
Siberian	Global	Study-wide	6	C=0.5	G=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 4	NC_000004.12:g.775060C>G
GRCh38.p14 chr 4	NC_000004.12:g.775060C>T
GRCh37.p13 chr 4	NC_000004.11:g.768848C>G
GRCh37.p13 chr 4	NC_000004.11:g.768848C>T

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.-2793+67… XM_047416472.1:c.-2793+6712G>C	N/A	Intron Variant
LOC124900163 transcript variant X3	XM_047416474.1:c.-2694+67… XM_047416474.1:c.-2694+6712G>C	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	C=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.775060=	NC_000004.12:g.775060C>G	NC_000004.12:g.775060C>T
GRCh37.p13 chr 4	NC_000004.11:g.768848=	NC_000004.11:g.768848C>G	NC_000004.11:g.768848C>T
LOC124900163 transcript variant X1	XM_047416472.1:c.-2793+6712=	XM_047416472.1:c.-2793+6712G>C	XM_047416472.1:c.-2793+6712G>A
LOC124900163 transcript variant X3	XM_047416474.1:c.-2694+6712=	XM_047416474.1:c.-2694+6712G>C	XM_047416474.1:c.-2694+6712G>A

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#.

42 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6460000	Feb 20, 2003 (111)
2	GMI	ss277536605	May 04, 2012 (137)
3	GMI	ss284828336	Apr 25, 2013 (138)
4	1000GENOMES	ss331375183	May 09, 2011 (134)
5	SSMP	ss651001595	Apr 25, 2013 (138)
6	EVA-GONL	ss979665037	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1071210482	Aug 21, 2014 (142)
8	1000GENOMES	ss1308056917	Aug 21, 2014 (142)
9	DDI	ss1429737119	Apr 01, 2015 (144)
10	EVA_DECODE	ss1589161985	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1609221101	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1652215134	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1922895040	Feb 12, 2016 (147)
14	USC_VALOUEV	ss2150126729	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2259758581	Dec 20, 2016 (150)
16	SYSTEMSBIOZJU	ss2625511587	Nov 08, 2017 (151)
17	GRF	ss2705561314	Nov 08, 2017 (151)
18	GNOMAD	ss2804597489	Nov 08, 2017 (151)
19	SWEGEN	ss2993979563	Nov 08, 2017 (151)
20	CSHL	ss3345494319	Nov 08, 2017 (151)
21	BIOINF_KMB_FNS_UNIBA	ss3645770921	Oct 12, 2018 (152)
22	EGCUT_WGS	ss3661918700	Jul 13, 2019 (153)
23	EVA_DECODE	ss3711220199	Jul 13, 2019 (153)
24	ACPOP	ss3730771305	Jul 13, 2019 (153)
25	EVA	ss3761274363	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3804415403	Jul 13, 2019 (153)
27	SGDP_PRJ	ss3858004610	Apr 25, 2020 (154)
28	KRGDB	ss3904127406	Apr 25, 2020 (154)
29	KOGIC	ss3953335379	Apr 25, 2020 (154)
30	TOPMED	ss4599920457	Apr 26, 2021 (155)
31	TOPMED	ss4599920458	Apr 26, 2021 (155)
32	TOMMO_GENOMICS	ss5163778349	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5257713388	Oct 17, 2022 (156)
34	EVA	ss5346320513	Oct 17, 2022 (156)
35	HUGCELL_USP	ss5456673013	Oct 17, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5537999996	Oct 17, 2022 (156)
37	SANFORD_IMAGENETICS	ss5634157979	Oct 17, 2022 (156)
38	TOMMO_GENOMICS	ss5697299242	Oct 17, 2022 (156)
39	YY_MCH	ss5804670302	Oct 17, 2022 (156)
40	EVA	ss5843417151	Oct 17, 2022 (156)
41	EVA	ss5861784700	Oct 17, 2022 (156)
42	EVA	ss5962534108	Oct 17, 2022 (156)
43	1000Genomes	NC_000004.11 - 768848	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000004.12 - 775060	Oct 17, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 768848	Oct 12, 2018 (152)
46	Genetic variation in the Estonian population	NC_000004.11 - 768848	Oct 12, 2018 (152)
47	gnomAD - Genomes	NC_000004.12 - 775060	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000004.11 - 768848	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000004.11 - 768848	Apr 25, 2020 (154)
50	Korean Genome Project	NC_000004.12 - 775060	Apr 25, 2020 (154)
51	Northern Sweden	NC_000004.11 - 768848	Jul 13, 2019 (153)
52	Qatari	NC_000004.11 - 768848	Apr 25, 2020 (154)
53	SGDP_PRJ	NC_000004.11 - 768848	Apr 25, 2020 (154)
54	Siberian	NC_000004.11 - 768848	Apr 25, 2020 (154)
55	8.3KJPN	NC_000004.11 - 768848	Apr 26, 2021 (155)
56	14KJPN	NC_000004.12 - 775060	Oct 17, 2022 (156)
57	TopMed Submission ignored due to conflicting rows: Row 437298013 (NC_000004.12:775059:C:G 16136/264690) Row 437298014 (NC_000004.12:775059:C:T 1/264690)	-	Apr 26, 2021 (155)
58	TopMed Submission ignored due to conflicting rows: Row 437298013 (NC_000004.12:775059:C:G 16136/264690) Row 437298014 (NC_000004.12:775059:C:T 1/264690)	-	Apr 26, 2021 (155)
59	UK 10K study - Twins	NC_000004.11 - 768848	Oct 12, 2018 (152)
60	A Vietnamese Genetic Variation Database	NC_000004.11 - 768848	Jul 13, 2019 (153)
61	ALFA	NC_000004.12 - 775060	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
ss277536605, ss284828336, ss1589161985	NC_000004.10:758847:C:G	NC_000004.12:775059:C:G	(self)
19393880, 10811853, 7656948, 4752459, 11304800, 4056170, 4936970, 10021590, 2643083, 21747656, 10811853, 2364150, ss331375183, ss651001595, ss979665037, ss1071210482, ss1308056917, ss1429737119, ss1609221101, ss1652215134, ss1922895040, ss2150126729, ss2625511587, ss2705561314, ss2804597489, ss2993979563, ss3345494319, ss3661918700, ss3730771305, ss3761274363, ss3858004610, ss3904127406, ss5163778349, ss5346320513, ss5634157979, ss5843417151, ss5962534108	NC_000004.11:768847:C:G	NC_000004.12:775059:C:G	(self)
25525931, 137683844, 9713380, 31136346, 4407252874, ss2259758581, ss3645770921, ss3711220199, ss3804415403, ss3953335379, ss4599920457, ss5257713388, ss5456673013, ss5537999996, ss5697299242, ss5804670302, ss5861784700	NC_000004.12:775059:C:G	NC_000004.12:775059:C:G	(self)
ss6460000	NT_037622.5:758847:C:G	NC_000004.12:775059:C:G	(self)
4407252874, ss4599920458	NC_000004.12:775059:C:T	NC_000004.12:775059:C:T	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2427157204	NC_000004.11:768847:C:T	NC_000004.12:775059:C:T

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

No publications for rs4690312

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

rs4690312