Name: rs6669335
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.

rs6669335

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:231598830 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.114996 (16116/140144, GnomAD)
A=0.06169 (1743/28256, 14KJPN)
A=0.05955 (998/16760, 8.3KJPN) (+ 16 more)
A=0.04752 (740/15572, ALFA)
A=0.1007 (645/6404, 1000G_30x)
A=0.0990 (496/5008, 1000G)
A=0.1549 (694/4480, Estonian)
A=0.1412 (544/3854, ALSPAC)
A=0.1475 (547/3708, TWINSUK)
A=0.0903 (264/2922, KOREAN)
A=0.0988 (181/1832, Korea1K)
A=0.162 (162/998, GoNL)
A=0.155 (93/600, NorthernSweden)
A=0.056 (12/216, Qatari)
A=0.107 (23/214, Vietnamese)
G=0.457 (53/116, SGDP_PRJ)
A=0.10 (4/40, GENOME_DK)
G=0.5 (4/8, Siberian)
A=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC00582 : Intron Variant
TSNAX-DISC1 : 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	15572	G=0.95248	A=0.04752, C=0.00000
European	Sub	11610	G=0.93902	A=0.06098, C=0.00000
African	Sub	2604	G=0.9988	A=0.0012, C=0.0000
African Others	Sub	104	G=1.000	A=0.000, C=0.000
African American	Sub	2500	G=0.9988	A=0.0012, C=0.0000
Asian	Sub	78	G=1.00	A=0.00, C=0.00
East Asian	Sub	64	G=1.00	A=0.00, C=0.00
Other Asian	Sub	14	G=1.00	A=0.00, C=0.00
Latin American 1	Sub	106	G=1.000	A=0.000, C=0.000
Latin American 2	Sub	506	G=1.000	A=0.000, C=0.000
South Asian	Sub	62	G=1.00	A=0.00, C=0.00
Other	Sub	606	G=0.952	A=0.048, C=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	140144	G=0.885004	A=0.114996
gnomAD - Genomes	European	Sub	75880	G=0.85028	A=0.14972
gnomAD - Genomes	African	Sub	42010	G=0.93844	A=0.06156
gnomAD - Genomes	American	Sub	13648	G=0.91486	A=0.08514
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.8727	A=0.1273
gnomAD - Genomes	East Asian	Sub	3132	G=0.8876	A=0.1124
gnomAD - Genomes	Other	Sub	2152	G=0.8922	A=0.1078
14KJPN	JAPANESE	Study-wide	28256	G=0.93831	A=0.06169
8.3KJPN	JAPANESE	Study-wide	16760	G=0.94045	A=0.05955
Allele Frequency Aggregator	Total	Global	15572	G=0.95248	A=0.04752, C=0.00000
Allele Frequency Aggregator	European	Sub	11610	G=0.93902	A=0.06098, C=0.00000
Allele Frequency Aggregator	African	Sub	2604	G=0.9988	A=0.0012, C=0.0000
Allele Frequency Aggregator	Other	Sub	606	G=0.952	A=0.048, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	506	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	106	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	78	G=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	62	G=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8993	A=0.1007
1000Genomes_30x	African	Sub	1786	G=0.9558	A=0.0442
1000Genomes_30x	Europe	Sub	1266	G=0.8602	A=0.1398
1000Genomes_30x	South Asian	Sub	1202	G=0.8611	A=0.1389
1000Genomes_30x	East Asian	Sub	1170	G=0.8752	A=0.1248
1000Genomes_30x	American	Sub	980	G=0.922	A=0.078
1000Genomes	Global	Study-wide	5008	G=0.9010	A=0.0990
1000Genomes	African	Sub	1322	G=0.9576	A=0.0424
1000Genomes	East Asian	Sub	1008	G=0.8800	A=0.1200
1000Genomes	Europe	Sub	1006	G=0.8658	A=0.1342
1000Genomes	South Asian	Sub	978	G=0.864	A=0.136
1000Genomes	American	Sub	694	G=0.927	A=0.073
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8451	A=0.1549
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8588	A=0.1412
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8525	A=0.1475
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9097	A=0.0903
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9012	A=0.0988
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.838	A=0.162
Northern Sweden	ACPOP	Study-wide	600	G=0.845	A=0.155
Qatari	Global	Study-wide	216	G=0.944	A=0.056
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.893	A=0.107
SGDP_PRJ	Global	Study-wide	116	G=0.457	A=0.543
The Danish reference pan genome	Danish	Study-wide	40	G=0.90	A=0.10
Siberian	Global	Study-wide	8	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 1	NC_000001.11:g.231598830G>A
GRCh38.p14 chr 1	NC_000001.11:g.231598830G>C
GRCh37.p13 chr 1	NC_000001.10:g.231734576G>A
GRCh37.p13 chr 1	NC_000001.10:g.231734576G>C

Gene: TSNAX-DISC1, TSNAX-DISC1 readthrough (NMD candidate) (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TSNAX-DISC1 transcript variant 1	NR_028393.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 2	NR_028394.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 3	NR_028395.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 4	NR_028396.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 5	NR_028397.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 6	NR_028398.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 7	NR_028399.1:n.	N/A	Intron Variant
TSNAX-DISC1 transcript variant 8	NR_028400.1:n.	N/A	Intron Variant

Gene: LINC00582, long intergenic non-protein coding RNA 582 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00582 transcript	NR_034037.1:n.	N/A	Intron 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	C
GRCh38.p14 chr 1	NC_000001.11:g.231598830=	NC_000001.11:g.231598830G>A	NC_000001.11:g.231598830G>C
GRCh37.p13 chr 1	NC_000001.10:g.231734576=	NC_000001.10:g.231734576G>A	NC_000001.10:g.231734576G>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#.

60 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9834621	Jul 11, 2003 (116)
2	HGSV	ss78769855	Dec 06, 2007 (129)
3	1000GENOMES	ss109026423	Jan 23, 2009 (130)
4	GMI	ss156408986	Dec 01, 2009 (138)
5	COMPLETE_GENOMICS	ss165890710	Jul 04, 2010 (132)
6	COMPLETE_GENOMICS	ss167561088	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss205305621	Jul 04, 2010 (132)
8	1000GENOMES	ss218937212	Jul 14, 2010 (132)
9	1000GENOMES	ss230943615	Jul 14, 2010 (132)
10	1000GENOMES	ss238549739	Jul 15, 2010 (132)
11	GMI	ss276258598	May 04, 2012 (137)
12	GMI	ss284246218	Apr 25, 2013 (138)
13	TISHKOFF	ss555204508	Apr 25, 2013 (138)
14	SSMP	ss648777441	Apr 25, 2013 (138)
15	EVA-GONL	ss976253211	Aug 21, 2014 (142)
16	1000GENOMES	ss1295060478	Aug 21, 2014 (142)
17	DDI	ss1426142863	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1574747124	Apr 01, 2015 (144)
19	EVA_DECODE	ss1585652895	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1602358347	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1645352380	Apr 01, 2015 (144)
22	HAMMER_LAB	ss1795874097	Sep 08, 2015 (146)
23	WEILL_CORNELL_DGM	ss1919474458	Feb 12, 2016 (147)
24	JJLAB	ss2020262581	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2148298620	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2170932623	Dec 20, 2016 (150)
27	GRF	ss2698298738	Nov 08, 2017 (151)
28	GNOMAD	ss2767381779	Nov 08, 2017 (151)
29	AFFY	ss2985540733	Nov 08, 2017 (151)
30	SWEGEN	ss2988619606	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3023892158	Nov 08, 2017 (151)
32	CSHL	ss3343959888	Nov 08, 2017 (151)
33	EGCUT_WGS	ss3656578352	Jul 12, 2019 (153)
34	EVA_DECODE	ss3688831821	Jul 12, 2019 (153)
35	ACPOP	ss3727951751	Jul 12, 2019 (153)
36	EVA	ss3747465696	Jul 12, 2019 (153)
37	PACBIO	ss3783715124	Jul 12, 2019 (153)
38	PACBIO	ss3789322786	Jul 12, 2019 (153)
39	PACBIO	ss3794195195	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3800467634	Jul 12, 2019 (153)
41	EVA	ss3826697307	Apr 25, 2020 (154)
42	EVA	ss3836750382	Apr 25, 2020 (154)
43	EVA	ss3842162830	Apr 25, 2020 (154)
44	SGDP_PRJ	ss3851111758	Apr 25, 2020 (154)
45	KRGDB	ss3896459527	Apr 25, 2020 (154)
46	KOGIC	ss3946706797	Apr 25, 2020 (154)
47	TOPMED	ss4487175857	Apr 25, 2021 (155)
48	TOPMED	ss4487175858	Apr 25, 2021 (155)
49	TOMMO_GENOMICS	ss5148904360	Apr 25, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5246154259	Oct 13, 2022 (156)
51	EVA	ss5325445183	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5446554446	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5520431645	Oct 13, 2022 (156)
54	SANFORD_IMAGENETICS	ss5627650166	Oct 13, 2022 (156)
55	TOMMO_GENOMICS	ss5676801920	Oct 13, 2022 (156)
56	YY_MCH	ss5801730691	Oct 13, 2022 (156)
57	EVA	ss5833407450	Oct 13, 2022 (156)
58	EVA	ss5849331229	Oct 13, 2022 (156)
59	EVA	ss5912386827	Oct 13, 2022 (156)
60	EVA	ss5939498420	Oct 13, 2022 (156)
61	1000Genomes	NC_000001.10 - 231734576	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000001.11 - 231598830	Oct 13, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 231734576	Oct 11, 2018 (152)
64	Genetic variation in the Estonian population	NC_000001.10 - 231734576	Oct 11, 2018 (152)
65	The Danish reference pan genome	NC_000001.10 - 231734576	Apr 25, 2020 (154)
66	gnomAD - Genomes	NC_000001.11 - 231598830	Apr 25, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000001.10 - 231734576	Apr 25, 2020 (154)
68	KOREAN population from KRGDB	NC_000001.10 - 231734576	Apr 25, 2020 (154)
69	Korean Genome Project	NC_000001.11 - 231598830	Apr 25, 2020 (154)
70	Northern Sweden	NC_000001.10 - 231734576	Jul 12, 2019 (153)
71	Qatari	NC_000001.10 - 231734576	Apr 25, 2020 (154)
72	SGDP_PRJ	NC_000001.10 - 231734576	Apr 25, 2020 (154)
73	Siberian	NC_000001.10 - 231734576	Apr 25, 2020 (154)
74	8.3KJPN	NC_000001.10 - 231734576	Apr 25, 2021 (155)
75	14KJPN	NC_000001.11 - 231598830	Oct 13, 2022 (156)
76	TopMed Submission ignored due to conflicting rows: Row 50782192 (NC_000001.11:231598829:G:A 29359/264690) Row 50782193 (NC_000001.11:231598829:G:C 4/264690)	-	Apr 25, 2021 (155)
77	TopMed Submission ignored due to conflicting rows: Row 50782192 (NC_000001.11:231598829:G:A 29359/264690) Row 50782193 (NC_000001.11:231598829:G:C 4/264690)	-	Apr 25, 2021 (155)
78	UK 10K study - Twins	NC_000001.10 - 231734576	Oct 11, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000001.10 - 231734576	Jul 12, 2019 (153)
80	ALFA	NC_000001.11 - 231598830	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)
rs76608077	Apr 25, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78769855	NC_000001.8:228041310:G:A	NC_000001.11:231598829:G:A	(self)
ss109026423, ss165890710, ss167561088, ss205305621, ss276258598, ss284246218, ss1585652895	NC_000001.9:229801198:G:A	NC_000001.11:231598829:G:A	(self)
5929908, 3279085, 2316600, 1927997, 1433369, 3636921, 1236616, 1516388, 3128738, 814974, 6873667, 3279085, 713290, ss218937212, ss230943615, ss238549739, ss555204508, ss648777441, ss976253211, ss1295060478, ss1426142863, ss1574747124, ss1602358347, ss1645352380, ss1795874097, ss1919474458, ss2020262581, ss2148298620, ss2698298738, ss2767381779, ss2985540733, ss2988619606, ss3343959888, ss3656578352, ss3727951751, ss3747465696, ss3783715124, ss3789322786, ss3794195195, ss3826697307, ss3836750382, ss3851111758, ss3896459527, ss5148904360, ss5325445183, ss5627650166, ss5833407450, ss5939498420	NC_000001.10:231734575:G:A	NC_000001.11:231598829:G:A	(self)
7957580, 42541568, 3084798, 10639024, 72385807, ss2170932623, ss3023892158, ss3688831821, ss3800467634, ss3842162830, ss3946706797, ss4487175857, ss5246154259, ss5446554446, ss5520431645, ss5676801920, ss5801730691, ss5849331229, ss5912386827	NC_000001.11:231598829:G:A	NC_000001.11:231598829:G:A	(self)
ss9834621	NT_021973.15:1665564:G:A	NC_000001.11:231598829:G:A	(self)
ss156408986	NT_167186.1:25252354:G:A	NC_000001.11:231598829:G:A	(self)
72385807, ss4487175858	NC_000001.11:231598829:G:C	NC_000001.11:231598829:G:C	(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 rs6669335

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

rs6669335