Name: rs6089763
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.

rs6089763

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:63677001 (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=0.120303 (31843/264690, TOPMED)
T=0.117354 (16445/140132, GnomAD)
T=0.12094 (9517/78690, PAGE_STUDY) (+ 18 more)
T=0.12735 (4568/35870, ALFA)
T=0.25526 (7213/28258, 14KJPN)
T=0.25847 (4332/16760, 8.3KJPN)
T=0.1627 (1042/6404, 1000G_30x)
T=0.1657 (830/5008, 1000G)
T=0.1237 (554/4480, Estonian)
T=0.1482 (571/3854, ALSPAC)
T=0.1535 (569/3708, TWINSUK)
T=0.3188 (934/2930, KOREAN)
T=0.3204 (587/1832, Korea1K)
T=0.181 (181/998, GoNL)
T=0.177 (106/600, NorthernSweden)
T=0.069 (15/216, Qatari)
T=0.302 (64/212, Vietnamese)
C=0.444 (79/178, SGDP_PRJ)
T=0.20 (8/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RTEL1 : Intron Variant
RTEL1-TNFRSF6B : Intron Variant
LOC124904954 : 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	35870	C=0.87265	T=0.12735
European	Sub	30418	C=0.86459	T=0.13541
African	Sub	3378	C=0.9559	T=0.0441
African Others	Sub	114	C=0.982	T=0.018
African American	Sub	3264	C=0.9550	T=0.0450
Asian	Sub	190	C=0.705	T=0.295
East Asian	Sub	164	C=0.707	T=0.293
Other Asian	Sub	26	C=0.69	T=0.31
Latin American 1	Sub	146	C=0.932	T=0.068
Latin American 2	Sub	610	C=0.843	T=0.157
South Asian	Sub	104	C=0.837	T=0.163
Other	Sub	1024	C=0.8818	T=0.1182

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	C=0.879697	T=0.120303
gnomAD - Genomes	Global	Study-wide	140132	C=0.882646	T=0.117354
gnomAD - Genomes	European	Sub	75882	C=0.85665	T=0.14335
gnomAD - Genomes	African	Sub	42014	C=0.95563	T=0.04437
gnomAD - Genomes	American	Sub	13646	C=0.84611	T=0.15389
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.9004	T=0.0996
gnomAD - Genomes	East Asian	Sub	3118	C=0.6719	T=0.3281
gnomAD - Genomes	Other	Sub	2150	C=0.8842	T=0.1158
The PAGE Study	Global	Study-wide	78690	C=0.87906	T=0.12094
The PAGE Study	AfricanAmerican	Sub	32514	C=0.95340	T=0.04660
The PAGE Study	Mexican	Sub	10810	C=0.81702	T=0.18298
The PAGE Study	Asian	Sub	8316	C=0.7244	T=0.2756
The PAGE Study	PuertoRican	Sub	7916	C=0.9042	T=0.0958
The PAGE Study	NativeHawaiian	Sub	4532	C=0.7785	T=0.2215
The PAGE Study	Cuban	Sub	4228	C=0.8981	T=0.1019
The PAGE Study	Dominican	Sub	3828	C=0.9323	T=0.0677
The PAGE Study	CentralAmerican	Sub	2448	C=0.7945	T=0.2055
The PAGE Study	SouthAmerican	Sub	1982	C=0.7901	T=0.2099
The PAGE Study	NativeAmerican	Sub	1260	C=0.8532	T=0.1468
The PAGE Study	SouthAsian	Sub	856	C=0.794	T=0.206
Allele Frequency Aggregator	Total	Global	35870	C=0.87265	T=0.12735
Allele Frequency Aggregator	European	Sub	30418	C=0.86459	T=0.13541
Allele Frequency Aggregator	African	Sub	3378	C=0.9559	T=0.0441
Allele Frequency Aggregator	Other	Sub	1024	C=0.8818	T=0.1182
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.843	T=0.157
Allele Frequency Aggregator	Asian	Sub	190	C=0.705	T=0.295
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.932	T=0.068
Allele Frequency Aggregator	South Asian	Sub	104	C=0.837	T=0.163
14KJPN	JAPANESE	Study-wide	28258	C=0.74474	T=0.25526
8.3KJPN	JAPANESE	Study-wide	16760	C=0.74153	T=0.25847
1000Genomes_30x	Global	Study-wide	6404	C=0.8373	T=0.1627
1000Genomes_30x	African	Sub	1786	C=0.9726	T=0.0274
1000Genomes_30x	Europe	Sub	1266	C=0.8768	T=0.1232
1000Genomes_30x	South Asian	Sub	1202	C=0.7662	T=0.2338
1000Genomes_30x	East Asian	Sub	1170	C=0.6880	T=0.3120
1000Genomes_30x	American	Sub	980	C=0.805	T=0.195
1000Genomes	Global	Study-wide	5008	C=0.8343	T=0.1657
1000Genomes	African	Sub	1322	C=0.9705	T=0.0295
1000Genomes	East Asian	Sub	1008	C=0.6984	T=0.3016
1000Genomes	Europe	Sub	1006	C=0.8688	T=0.1312
1000Genomes	South Asian	Sub	978	C=0.777	T=0.223
1000Genomes	American	Sub	694	C=0.803	T=0.197
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8763	T=0.1237
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8518	T=0.1482
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8465	T=0.1535
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6812	G=0.0000, T=0.3188
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6796	T=0.3204
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.819	T=0.181
Northern Sweden	ACPOP	Study-wide	600	C=0.823	T=0.177
Qatari	Global	Study-wide	216	C=0.931	T=0.069
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.698	T=0.302
SGDP_PRJ	Global	Study-wide	178	C=0.444	T=0.556
The Danish reference pan genome	Danish	Study-wide	40	C=0.80	T=0.20
Siberian	Global	Study-wide	12	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 20	NC_000020.11:g.63677001C>G
GRCh38.p14 chr 20	NC_000020.11:g.63677001C>T
GRCh37.p13 chr 20	NC_000020.10:g.62308354C>G
GRCh37.p13 chr 20	NC_000020.10:g.62308354C>T
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.24192C>G
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.24192C>T

Gene: RTEL1, regulator of telomere elongation helicase 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RTEL1 transcript variant 3	NM_001283009.2:c.920-1144… NM_001283009.2:c.920-1144C>G	N/A	Intron Variant
RTEL1 transcript variant 4	NM_001283010.1:c.251-1144… NM_001283010.1:c.251-1144C>G	N/A	Intron Variant
RTEL1 transcript variant 1	NM_016434.4:c.920-1144C>G	N/A	Intron Variant
RTEL1 transcript variant 2	NM_032957.5:c.992-1144C>G	N/A	Intron Variant

Gene: RTEL1-TNFRSF6B, RTEL1-TNFRSF6B readthrough (NMD candidate) (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RTEL1-TNFRSF6B transcript	NR_037882.1:n.	N/A	Intron Variant

Gene: LOC124904954, uncharacterized LOC124904954 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124904954 transcript	XR_007067717.1: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	C=	G	T
GRCh38.p14 chr 20	NC_000020.11:g.63677001=	NC_000020.11:g.63677001C>G	NC_000020.11:g.63677001C>T
GRCh37.p13 chr 20	NC_000020.10:g.62308354=	NC_000020.10:g.62308354C>G	NC_000020.10:g.62308354C>T
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.24192=	NG_033901.1:g.24192C>G	NG_033901.1:g.24192C>T
RTEL1 transcript variant 3	NM_001283009.2:c.920-1144=	NM_001283009.2:c.920-1144C>G	NM_001283009.2:c.920-1144C>T
RTEL1 transcript variant 4	NM_001283010.1:c.251-1144=	NM_001283010.1:c.251-1144C>G	NM_001283010.1:c.251-1144C>T
RTEL1 transcript variant 1	NM_016434.3:c.920-1144=	NM_016434.3:c.920-1144C>G	NM_016434.3:c.920-1144C>T
RTEL1 transcript variant 1	NM_016434.4:c.920-1144=	NM_016434.4:c.920-1144C>G	NM_016434.4:c.920-1144C>T
RTEL1 transcript variant 2	NM_032957.4:c.992-1144=	NM_032957.4:c.992-1144C>G	NM_032957.4:c.992-1144C>T
RTEL1 transcript variant 2	NM_032957.5:c.992-1144=	NM_032957.5:c.992-1144C>G	NM_032957.5:c.992-1144C>T
RTEL1 transcript variant X1	XM_005260207.1:c.920-1144=	XM_005260207.1:c.920-1144C>G	XM_005260207.1:c.920-1144C>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#.

67 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8413247	Apr 21, 2003 (114)
2	CSHL-HAPMAP	ss19477578	Feb 27, 2004 (120)
3	ABI	ss41379191	Mar 13, 2006 (126)
4	HGSV	ss78263513	Dec 07, 2007 (129)
5	HUMANGENOME_JCVI	ss96241481	Feb 05, 2009 (130)
6	1000GENOMES	ss112248626	Jan 25, 2009 (130)
7	ENSEMBL	ss135675500	Dec 01, 2009 (131)
8	BCM-HGSC-SUB	ss208747697	Jul 04, 2010 (132)
9	1000GENOMES	ss228452656	Jul 14, 2010 (132)
10	1000GENOMES	ss237902419	Jul 15, 2010 (132)
11	1000GENOMES	ss244057809	Jul 15, 2010 (132)
12	GMI	ss283446511	May 04, 2012 (137)
13	GMI	ss287486361	Apr 25, 2013 (138)
14	SSMP	ss662250223	Apr 25, 2013 (138)
15	EVA-GONL	ss994910403	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1082340186	Aug 21, 2014 (142)
17	1000GENOMES	ss1365496916	Aug 21, 2014 (142)
18	EVA_GENOME_DK	ss1579578617	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1639168283	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1682162316	Apr 01, 2015 (144)
21	EVA_DECODE	ss1698975171	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1938433730	Feb 12, 2016 (147)
23	ILLUMINA	ss1959934152	Feb 12, 2016 (147)
24	GENOMED	ss1969172388	Jul 19, 2016 (147)
25	JJLAB	ss2029997156	Sep 14, 2016 (149)
26	ILLUMINA	ss2094920342	Dec 20, 2016 (150)
27	ILLUMINA	ss2095117329	Dec 20, 2016 (150)
28	USC_VALOUEV	ss2158569253	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2244249929	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2629490938	Nov 08, 2017 (151)
31	GRF	ss2704266712	Nov 08, 2017 (151)
32	ILLUMINA	ss2710945336	Nov 08, 2017 (151)
33	GNOMAD	ss2969449552	Nov 08, 2017 (151)
34	AFFY	ss2985223138	Nov 08, 2017 (151)
35	SWEGEN	ss3018478514	Nov 08, 2017 (151)
36	ILLUMINA	ss3022138783	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3028831984	Nov 08, 2017 (151)
38	CSHL	ss3352597554	Nov 08, 2017 (151)
39	URBANLAB	ss3651056229	Oct 12, 2018 (152)
40	ILLUMINA	ss3652596908	Oct 12, 2018 (152)
41	ILLUMINA	ss3652596909	Oct 12, 2018 (152)
42	EGCUT_WGS	ss3685163586	Jul 13, 2019 (153)
43	EVA_DECODE	ss3707317613	Jul 13, 2019 (153)
44	ILLUMINA	ss3725932166	Jul 13, 2019 (153)
45	ACPOP	ss3743554180	Jul 13, 2019 (153)
46	EVA	ss3758871734	Jul 13, 2019 (153)
47	PAGE_CC	ss3772061876	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3822025198	Jul 13, 2019 (153)
49	EVA	ss3835766232	Apr 27, 2020 (154)
50	EVA	ss3841508000	Apr 27, 2020 (154)
51	EVA	ss3847021829	Apr 27, 2020 (154)
52	SGDP_PRJ	ss3889491810	Apr 27, 2020 (154)
53	KRGDB	ss3939819597	Apr 27, 2020 (154)
54	KOGIC	ss3982646680	Apr 27, 2020 (154)
55	TOPMED	ss5094760316	Apr 27, 2021 (155)
56	TOMMO_GENOMICS	ss5230477776	Apr 27, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5309444434	Oct 16, 2022 (156)
58	EVA	ss5438586462	Oct 16, 2022 (156)
59	HUGCELL_USP	ss5501658958	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5616203204	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5663573170	Oct 16, 2022 (156)
62	TOMMO_GENOMICS	ss5790544899	Oct 16, 2022 (156)
63	YY_MCH	ss5818201963	Oct 16, 2022 (156)
64	EVA	ss5845947966	Oct 16, 2022 (156)
65	EVA	ss5853217820	Oct 16, 2022 (156)
66	EVA	ss5924168513	Oct 16, 2022 (156)
67	EVA	ss5958506347	Oct 16, 2022 (156)
68	1000Genomes	NC_000020.10 - 62308354	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000020.11 - 63677001	Oct 16, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 62308354	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000020.10 - 62308354	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000020.10 - 62308354	Apr 27, 2020 (154)
73	gnomAD - Genomes	NC_000020.11 - 63677001	Apr 27, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000020.10 - 62308354	Apr 27, 2020 (154)
75	KOREAN population from KRGDB	NC_000020.10 - 62308354	Apr 27, 2020 (154)
76	Korean Genome Project	NC_000020.11 - 63677001	Apr 27, 2020 (154)
77	Northern Sweden	NC_000020.10 - 62308354	Jul 13, 2019 (153)
78	The PAGE Study	NC_000020.11 - 63677001	Jul 13, 2019 (153)
79	Qatari	NC_000020.10 - 62308354	Apr 27, 2020 (154)
80	SGDP_PRJ	NC_000020.10 - 62308354	Apr 27, 2020 (154)
81	Siberian	NC_000020.10 - 62308354	Apr 27, 2020 (154)
82	8.3KJPN	NC_000020.10 - 62308354	Apr 27, 2021 (155)
83	14KJPN	NC_000020.11 - 63677001	Oct 16, 2022 (156)
84	TopMed	NC_000020.11 - 63677001	Apr 27, 2021 (155)
85	UK 10K study - Twins	NC_000020.10 - 62308354	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000020.10 - 62308354	Jul 13, 2019 (153)
87	ALFA	NC_000020.11 - 63677001	Apr 27, 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
46996991, ss3939819597	NC_000020.10:62308353:C:G	NC_000020.11:63677000:C:G	(self)
ss78263513, ss112248626, ss208747697, ss283446511, ss287486361, ss1698975171, ss2094920342	NC_000020.9:61778797:C:T	NC_000020.11:63677000:C:T	(self)
78985299, 43733833, 30901834, 5743556, 19475814, 46996991, 16839045, 20475652, 41508790, 11085607, 88447083, 43733833, 9643715, ss228452656, ss237902419, ss244057809, ss662250223, ss994910403, ss1082340186, ss1365496916, ss1579578617, ss1639168283, ss1682162316, ss1938433730, ss1959934152, ss1969172388, ss2029997156, ss2095117329, ss2158569253, ss2629490938, ss2704266712, ss2710945336, ss2969449552, ss2985223138, ss3018478514, ss3022138783, ss3352597554, ss3652596908, ss3652596909, ss3685163586, ss3743554180, ss3758871734, ss3835766232, ss3841508000, ss3889491810, ss3939819597, ss5230477776, ss5438586462, ss5663573170, ss5845947966, ss5958506347	NC_000020.10:62308353:C:T	NC_000020.11:63677000:C:T	(self)
103729139, 557015141, 39024681, 1283345, 124382003, 369869261, 8607122343, ss2244249929, ss3028831984, ss3651056229, ss3707317613, ss3725932166, ss3772061876, ss3822025198, ss3847021829, ss3982646680, ss5094760316, ss5309444434, ss5501658958, ss5616203204, ss5790544899, ss5818201963, ss5853217820, ss5924168513	NC_000020.11:63677000:C:T	NC_000020.11:63677000:C:T	(self)
ss8413247, ss19477578	NT_011333.5:1044983:C:T	NC_000020.11:63677000:C:T	(self)
ss41379191, ss96241481, ss135675500	NT_011333.6:1044984:C:T	NC_000020.11:63677000: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 rs6089763

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

rs6089763