Name: rs6828898
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.

rs6828898

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:771323 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.066145 (8466/127992, GnomAD)
A=0.11769 (3304/28074, 14KJPN)
A=0.12149 (2034/16742, 8.3KJPN) (+ 14 more)
A=0.06556 (1095/16702, ALFA)
A=0.0923 (591/6404, 1000G_30x)
A=0.0958 (480/5008, 1000G)
A=0.0810 (363/4480, Estonian)
A=0.0547 (211/3854, ALSPAC)
A=0.0564 (209/3708, TWINSUK)
A=0.1521 (445/2926, KOREAN)
A=0.061 (61/998, GoNL)
A=0.048 (29/598, NorthernSweden)
A=0.111 (24/216, Qatari)
G=0.46 (35/76, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, 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	16702	G=0.93444	A=0.06556
European	Sub	12214	G=0.93000	A=0.07000
African	Sub	2864	G=0.9490	A=0.0510
African Others	Sub	108	G=0.935	A=0.065
African American	Sub	2756	G=0.9496	A=0.0504
Asian	Sub	108	G=0.898	A=0.102
East Asian	Sub	84	G=0.88	A=0.12
Other Asian	Sub	24	G=0.96	A=0.04
Latin American 1	Sub	146	G=0.932	A=0.068
Latin American 2	Sub	610	G=0.969	A=0.031
South Asian	Sub	94	G=0.85	A=0.15
Other	Sub	666	G=0.940	A=0.060

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
gnomAD - Genomes	Global	Study-wide	127992	G=0.933855	A=0.066145
gnomAD - Genomes	European	Sub	71444	G=0.92849	A=0.07151
gnomAD - Genomes	African	Sub	36984	G=0.94984	A=0.05016
gnomAD - Genomes	American	Sub	11294	G=0.94342	A=0.05658
gnomAD - Genomes	Ashkenazi Jewish	Sub	3268	G=0.8966	A=0.1034
gnomAD - Genomes	East Asian	Sub	3056	G=0.8747	A=0.1253
gnomAD - Genomes	Other	Sub	1946	G=0.9270	A=0.0730
14KJPN	JAPANESE	Study-wide	28074	G=0.88231	A=0.11769
8.3KJPN	JAPANESE	Study-wide	16742	G=0.87851	A=0.12149
Allele Frequency Aggregator	Total	Global	16702	G=0.93444	A=0.06556
Allele Frequency Aggregator	European	Sub	12214	G=0.93000	A=0.07000
Allele Frequency Aggregator	African	Sub	2864	G=0.9490	A=0.0510
Allele Frequency Aggregator	Other	Sub	666	G=0.940	A=0.060
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.969	A=0.031
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.932	A=0.068
Allele Frequency Aggregator	Asian	Sub	108	G=0.898	A=0.102
Allele Frequency Aggregator	South Asian	Sub	94	G=0.85	A=0.15
1000Genomes_30x	Global	Study-wide	6404	G=0.9077	A=0.0923
1000Genomes_30x	African	Sub	1786	G=0.9524	A=0.0476
1000Genomes_30x	Europe	Sub	1266	G=0.9273	A=0.0727
1000Genomes_30x	South Asian	Sub	1202	G=0.8103	A=0.1897
1000Genomes_30x	East Asian	Sub	1170	G=0.8786	A=0.1214
1000Genomes_30x	American	Sub	980	G=0.955	A=0.045
1000Genomes	Global	Study-wide	5008	G=0.9042	A=0.0958
1000Genomes	African	Sub	1322	G=0.9539	A=0.0461
1000Genomes	East Asian	Sub	1008	G=0.8780	A=0.1220
1000Genomes	Europe	Sub	1006	G=0.9245	A=0.0755
1000Genomes	South Asian	Sub	978	G=0.807	A=0.193
1000Genomes	American	Sub	694	G=0.955	A=0.045
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9190	A=0.0810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9453	A=0.0547
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9436	A=0.0564
KOREAN population from KRGDB	KOREAN	Study-wide	2926	G=0.8479	A=0.1521
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.939	A=0.061
Northern Sweden	ACPOP	Study-wide	598	G=0.952	A=0.048
Qatari	Global	Study-wide	216	G=0.889	A=0.111
SGDP_PRJ	Global	Study-wide	76	G=0.46	A=0.54
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
Siberian	Global	Study-wide	2	G=0.5	A=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.771323G>A
GRCh38.p14 chr 4	NC_000004.12:g.771323G>T
GRCh37.p13 chr 4	NC_000004.11:g.765111G>A
GRCh37.p13 chr 4	NC_000004.11:g.765111G>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.-2792-84… XM_047416472.1:c.-2792-8484C>T	N/A	Intron Variant
LOC124900163 transcript variant X3	XM_047416474.1:c.-2693-85… XM_047416474.1:c.-2693-8583C>T	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	G=	A	T
GRCh38.p14 chr 4	NC_000004.12:g.771323=	NC_000004.12:g.771323G>A	NC_000004.12:g.771323G>T
GRCh37.p13 chr 4	NC_000004.11:g.765111=	NC_000004.11:g.765111G>A	NC_000004.11:g.765111G>T
LOC124900163 transcript variant X1	XM_047416472.1:c.-2792-8484=	XM_047416472.1:c.-2792-8484C>T	XM_047416472.1:c.-2792-8484C>A
LOC124900163 transcript variant X3	XM_047416474.1:c.-2693-8583=	XM_047416474.1:c.-2693-8583C>T	XM_047416474.1:c.-2693-8583C>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#.

41 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10134523	Jul 11, 2003 (116)
2	BL	ss252869499	May 09, 2011 (134)
3	1000GENOMES	ss331375157	May 09, 2011 (134)
4	GMI	ss475647257	May 04, 2012 (137)
5	SSMP	ss651001565	Apr 25, 2013 (138)
6	EVA-GONL	ss979664990	Aug 21, 2014 (142)
7	1000GENOMES	ss1308056731	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1580377522	Apr 01, 2015 (144)
9	EVA_DECODE	ss1589161944	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1609221031	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1652215064	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1922894985	Feb 12, 2016 (147)
13	USC_VALOUEV	ss2150126704	Dec 20, 2016 (150)
14	SYSTEMSBIOZJU	ss2625511572	Nov 08, 2017 (151)
15	GRF	ss2705561272	Nov 08, 2017 (151)
16	GNOMAD	ss2804596976	Nov 08, 2017 (151)
17	SWEGEN	ss2993979492	Nov 08, 2017 (151)
18	CSHL	ss3345494288	Nov 08, 2017 (151)
19	EGCUT_WGS	ss3661918640	Jul 13, 2019 (153)
20	EVA_DECODE	ss3711220096	Jul 13, 2019 (153)
21	EVA_DECODE	ss3711220097	Jul 13, 2019 (153)
22	ACPOP	ss3730771262	Jul 13, 2019 (153)
23	ILLUMINA	ss3744521176	Jul 13, 2019 (153)
24	EVA	ss3761274304	Jul 13, 2019 (153)
25	PACBIO	ss3784592572	Jul 13, 2019 (153)
26	PACBIO	ss3790066266	Jul 13, 2019 (153)
27	PACBIO	ss3794941305	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3804415350	Jul 13, 2019 (153)
29	SGDP_PRJ	ss3858004517	Apr 25, 2020 (154)
30	KRGDB	ss3904127269	Apr 25, 2020 (154)
31	TOMMO_GENOMICS	ss5163778110	Apr 26, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5257713206	Oct 17, 2022 (156)
33	EVA	ss5346320212	Oct 17, 2022 (156)
34	EVA	ss5507365766	Oct 17, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5537999771	Oct 17, 2022 (156)
36	SANFORD_IMAGENETICS	ss5634157891	Oct 17, 2022 (156)
37	TOMMO_GENOMICS	ss5697298929	Oct 17, 2022 (156)
38	YY_MCH	ss5804670258	Oct 17, 2022 (156)
39	EVA	ss5843417089	Oct 17, 2022 (156)
40	EVA	ss5861784513	Oct 17, 2022 (156)
41	EVA	ss5962534015	Oct 17, 2022 (156)
42	1000Genomes	NC_000004.11 - 765111	Oct 12, 2018 (152)
43	1000Genomes_30x	NC_000004.12 - 771323	Oct 17, 2022 (156)
44	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 765111	Oct 12, 2018 (152)
45	Genetic variation in the Estonian population	NC_000004.11 - 765111	Oct 12, 2018 (152)
46	The Danish reference pan genome	NC_000004.11 - 765111	Apr 25, 2020 (154)
47	gnomAD - Genomes	NC_000004.12 - 771323	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000004.11 - 765111	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000004.11 - 765111	Apr 25, 2020 (154)
50	Northern Sweden	NC_000004.11 - 765111	Jul 13, 2019 (153)
51	Qatari	NC_000004.11 - 765111	Apr 25, 2020 (154)
52	SGDP_PRJ	NC_000004.11 - 765111	Apr 25, 2020 (154)
53	Siberian	NC_000004.11 - 765111	Apr 25, 2020 (154)
54	8.3KJPN	NC_000004.11 - 765111	Apr 26, 2021 (155)
55	14KJPN	NC_000004.12 - 771323	Oct 17, 2022 (156)
56	UK 10K study - Twins	NC_000004.11 - 765111	Oct 12, 2018 (152)
57	ALFA	NC_000004.12 - 771323	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
ss252869499, ss475647257, ss1589161944	NC_000004.10:755110:G:A	NC_000004.12:771322:G:A	(self)
19393688, 10811775, 7656888, 6542461, 4752412, 11304663, 4056127, 4936915, 10021497, 2643058, 21747417, 10811775, ss331375157, ss651001565, ss979664990, ss1308056731, ss1580377522, ss1609221031, ss1652215064, ss1922894985, ss2150126704, ss2625511572, ss2705561272, ss2804596976, ss2993979492, ss3345494288, ss3661918640, ss3730771262, ss3744521176, ss3761274304, ss3784592572, ss3790066266, ss3794941305, ss3858004517, ss3904127269, ss5163778110, ss5346320212, ss5507365766, ss5634157891, ss5843417089, ss5962534015	NC_000004.11:765110:G:A	NC_000004.12:771322:G:A	(self)
25525706, 137682587, 31136033, 2958130072, ss3711220096, ss3804415350, ss5257713206, ss5537999771, ss5697298929, ss5804670258, ss5861784513	NC_000004.12:771322:G:A	NC_000004.12:771322:G:A	(self)
ss10134523	NT_037622.3:754940:G:A	NC_000004.12:771322:G:A	(self)
ss3711220097	NC_000004.12:771322:G:T	NC_000004.12:771322:G: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 rs6828898

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

rs6828898