Name: rs2738778
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.

rs2738778

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:63660477 (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=0.171586 (45417/264690, TOPMED)
T=0.169161 (23711/140168, GnomAD)
T=0.48273 (13641/28258, 14KJPN) (+ 16 more)
T=0.48628 (8150/16760, 8.3KJPN)
T=0.10052 (1551/15430, ALFA)
T=0.2110 (1351/6404, 1000G_30x)
T=0.2194 (1099/5008, 1000G)
T=0.1768 (792/4480, Estonian)
T=0.2317 (893/3854, ALSPAC)
T=0.2376 (881/3708, TWINSUK)
T=0.4730 (1386/2930, KOREAN)
T=0.4645 (851/1832, Korea1K)
T=0.267 (266/998, GoNL)
T=0.243 (146/600, NorthernSweden)
C=0.381 (102/268, SGDP_PRJ)
T=0.181 (39/216, Qatari)
T=0.362 (76/210, Vietnamese)
T=0.25 (10/40, GENOME_DK)
C=0.40 (12/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RTEL1 : Intron Variant
RTEL1-TNFRSF6B : 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	15430	C=0.89948	G=0.00000, T=0.10052
European	Sub	11554	C=0.87398	G=0.00000, T=0.12602
African	Sub	2706	C=0.9812	G=0.0000, T=0.0188
African Others	Sub	108	C=1.000	G=0.000, T=0.000
African American	Sub	2598	C=0.9804	G=0.0000, T=0.0196
Asian	Sub	34	C=0.88	G=0.00, T=0.12
East Asian	Sub	26	C=0.92	G=0.00, T=0.08
Other Asian	Sub	8	C=0.8	G=0.0, T=0.2
Latin American 1	Sub	106	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	418	C=1.000	G=0.000, T=0.000
South Asian	Sub	70	C=0.97	G=0.00, T=0.03
Other	Sub	542	C=0.930	G=0.000, T=0.070

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=0.828414	T=0.171586
gnomAD - Genomes	Global	Study-wide	140168	C=0.830839	T=0.169161
gnomAD - Genomes	European	Sub	75902	C=0.78458	T=0.21542
gnomAD - Genomes	African	Sub	42024	C=0.93806	T=0.06194
gnomAD - Genomes	American	Sub	13650	C=0.83172	T=0.16828
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.7797	T=0.2203
gnomAD - Genomes	East Asian	Sub	3128	C=0.5665	T=0.4335
gnomAD - Genomes	Other	Sub	2146	C=0.8262	T=0.1738
14KJPN	JAPANESE	Study-wide	28258	C=0.51727	T=0.48273
8.3KJPN	JAPANESE	Study-wide	16760	C=0.51372	T=0.48628
Allele Frequency Aggregator	Total	Global	15430	C=0.89948	G=0.00000, T=0.10052
Allele Frequency Aggregator	European	Sub	11554	C=0.87398	G=0.00000, T=0.12602
Allele Frequency Aggregator	African	Sub	2706	C=0.9812	G=0.0000, T=0.0188
Allele Frequency Aggregator	Other	Sub	542	C=0.930	G=0.000, T=0.070
Allele Frequency Aggregator	Latin American 2	Sub	418	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	106	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	70	C=0.97	G=0.00, T=0.03
Allele Frequency Aggregator	Asian	Sub	34	C=0.88	G=0.00, T=0.12
1000Genomes_30x	Global	Study-wide	6404	C=0.7890	T=0.2110
1000Genomes_30x	African	Sub	1786	C=0.9748	T=0.0252
1000Genomes_30x	Europe	Sub	1266	C=0.7986	T=0.2014
1000Genomes_30x	South Asian	Sub	1202	C=0.7379	T=0.2621
1000Genomes_30x	East Asian	Sub	1170	C=0.5231	T=0.4769
1000Genomes_30x	American	Sub	980	C=0.818	T=0.182
1000Genomes	Global	Study-wide	5008	C=0.7806	T=0.2194
1000Genomes	African	Sub	1322	C=0.9735	T=0.0265
1000Genomes	East Asian	Sub	1008	C=0.5159	T=0.4841
1000Genomes	Europe	Sub	1006	C=0.7972	T=0.2028
1000Genomes	South Asian	Sub	978	C=0.745	T=0.255
1000Genomes	American	Sub	694	C=0.823	T=0.177
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8232	T=0.1768
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7683	T=0.2317
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7624	T=0.2376
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5270	T=0.4730
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5355	T=0.4645
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.733	T=0.267
Northern Sweden	ACPOP	Study-wide	600	C=0.757	T=0.243
SGDP_PRJ	Global	Study-wide	268	C=0.381	T=0.619
Qatari	Global	Study-wide	216	C=0.819	T=0.181
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.638	T=0.362
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	30	C=0.40	T=0.60

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.63660477C>G
GRCh38.p14 chr 20	NC_000020.11:g.63660477C>T
GRCh37.p13 chr 20	NC_000020.10:g.62291830C>G
GRCh37.p13 chr 20	NC_000020.10:g.62291830C>T
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.7668C>G
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.7668C>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.103-821C… NM_001283009.2:c.103-821C>G	N/A	Intron Variant
RTEL1 transcript variant 4	NM_001283010.1:c.-567-821… NM_001283010.1:c.-567-821C>G	N/A	Intron Variant
RTEL1 transcript variant 1	NM_016434.4:c.103-821C>G	N/A	Intron Variant
RTEL1 transcript variant 2	NM_032957.5:c.103-821C>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

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.63660477=	NC_000020.11:g.63660477C>G	NC_000020.11:g.63660477C>T
GRCh37.p13 chr 20	NC_000020.10:g.62291830=	NC_000020.10:g.62291830C>G	NC_000020.10:g.62291830C>T
RTEL1 RefSeqGene (LRG_1149)	NG_033901.1:g.7668=	NG_033901.1:g.7668C>G	NG_033901.1:g.7668C>T
RTEL1 transcript variant 3	NM_001283009.2:c.103-821=	NM_001283009.2:c.103-821C>G	NM_001283009.2:c.103-821C>T
RTEL1 transcript variant 4	NM_001283010.1:c.-567-821=	NM_001283010.1:c.-567-821C>G	NM_001283010.1:c.-567-821C>T
RTEL1 transcript variant 1	NM_016434.3:c.103-821=	NM_016434.3:c.103-821C>G	NM_016434.3:c.103-821C>T
RTEL1 transcript variant 1	NM_016434.4:c.103-821=	NM_016434.4:c.103-821C>G	NM_016434.4:c.103-821C>T
RTEL1 transcript variant 2	NM_032957.4:c.103-821=	NM_032957.4:c.103-821C>G	NM_032957.4:c.103-821C>T
RTEL1 transcript variant 2	NM_032957.5:c.103-821=	NM_032957.5:c.103-821C>G	NM_032957.5:c.103-821C>T
RTEL1 transcript variant X1	XM_005260207.1:c.103-821=	XM_005260207.1:c.103-821C>G	XM_005260207.1:c.103-821C>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#.

61 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3866066	Sep 28, 2001 (100)
2	SC_SNP	ss8413246	Apr 21, 2003 (126)
3	SSAHASNP	ss21770136	Apr 05, 2004 (126)
4	ABI	ss41388631	Mar 11, 2006 (126)
5	HUMANGENOME_JCVI	ss96207149	Feb 03, 2009 (130)
6	COMPLETE_GENOMICS	ss168433702	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss208715683	Jul 04, 2010 (132)
8	1000GENOMES	ss237902349	Jul 15, 2010 (132)
9	1000GENOMES	ss244057770	Jul 15, 2010 (132)
10	BL	ss255774174	May 09, 2011 (134)
11	GMI	ss283446472	May 04, 2012 (137)
12	GMI	ss287486341	Apr 25, 2013 (138)
13	PJP	ss292599598	May 09, 2011 (134)
14	SSMP	ss662250106	Apr 25, 2013 (138)
15	EVA-GONL	ss994910208	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1082340076	Aug 21, 2014 (142)
17	1000GENOMES	ss1365496208	Aug 21, 2014 (142)
18	DDI	ss1429107017	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1579578532	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1639167943	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1682161976	Apr 01, 2015 (144)
22	EVA_DECODE	ss1698974998	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1938433527	Feb 12, 2016 (147)
24	JJLAB	ss2029997052	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2158569126	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2244248546	Dec 20, 2016 (150)
27	SYSTEMSBIOZJU	ss2629490911	Nov 08, 2017 (151)
28	GRF	ss2704266629	Nov 08, 2017 (151)
29	GNOMAD	ss2969447731	Nov 08, 2017 (151)
30	SWEGEN	ss3018478216	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3028831905	Nov 08, 2017 (151)
32	CSHL	ss3352597456	Nov 08, 2017 (151)
33	URBANLAB	ss3651056225	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3685163291	Jul 13, 2019 (153)
35	EVA_DECODE	ss3707317242	Jul 13, 2019 (153)
36	ACPOP	ss3743554010	Jul 13, 2019 (153)
37	EVA	ss3758871501	Jul 13, 2019 (153)
38	PACBIO	ss3788696232	Jul 13, 2019 (153)
39	PACBIO	ss3793580122	Jul 13, 2019 (153)
40	PACBIO	ss3798467582	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3822024982	Jul 13, 2019 (153)
42	EVA	ss3835766110	Apr 27, 2020 (154)
43	EVA	ss3841507962	Apr 27, 2020 (154)
44	EVA	ss3847021787	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3889491451	Apr 27, 2020 (154)
46	KRGDB	ss3939819176	Apr 27, 2020 (154)
47	KOGIC	ss3982646327	Apr 27, 2020 (154)
48	TOPMED	ss5094755220	Apr 27, 2021 (155)
49	TOMMO_GENOMICS	ss5230477036	Apr 27, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5309443819	Oct 16, 2022 (156)
51	EVA	ss5438585337	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5501658426	Oct 16, 2022 (156)
53	EVA	ss5512263916	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5616202303	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5663572816	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5790543934	Oct 16, 2022 (156)
57	YY_MCH	ss5818201825	Oct 16, 2022 (156)
58	EVA	ss5845947678	Oct 16, 2022 (156)
59	EVA	ss5853217770	Oct 16, 2022 (156)
60	EVA	ss5924167841	Oct 16, 2022 (156)
61	EVA	ss5958506010	Oct 16, 2022 (156)
62	1000Genomes	NC_000020.10 - 62291830	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000020.11 - 63660477	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 62291830	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000020.10 - 62291830	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000020.10 - 62291830	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000020.11 - 63660477	Apr 27, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000020.10 - 62291830	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000020.10 - 62291830	Apr 27, 2020 (154)
70	Korean Genome Project	NC_000020.11 - 63660477	Apr 27, 2020 (154)
71	Northern Sweden	NC_000020.10 - 62291830	Jul 13, 2019 (153)
72	Qatari	NC_000020.10 - 62291830	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000020.10 - 62291830	Apr 27, 2020 (154)
74	Siberian	NC_000020.10 - 62291830	Apr 27, 2020 (154)
75	8.3KJPN	NC_000020.10 - 62291830	Apr 27, 2021 (155)
76	14KJPN	NC_000020.11 - 63660477	Oct 16, 2022 (156)
77	TopMed	NC_000020.11 - 63660477	Apr 27, 2021 (155)
78	UK 10K study - Twins	NC_000020.10 - 62291830	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000020.10 - 62291830	Jul 13, 2019 (153)
80	ALFA	NC_000020.11 - 63660477	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).

Associated ID	History Updated (Build)
rs6089762	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
8743125077	NC_000020.11:63660476:C:G	NC_000020.11:63660476:C:G	(self)
ss168433702, ss208715683, ss255774174, ss283446472, ss287486341, ss292599598, ss1698974998	NC_000020.9:61762273:C:T	NC_000020.11:63660476:C:T	(self)
78984575, 43733469, 30901539, 5743471, 19475622, 46996570, 16838875, 20475449, 41508431, 11085480, 88446343, 43733469, 9643662, ss237902349, ss244057770, ss662250106, ss994910208, ss1082340076, ss1365496208, ss1429107017, ss1579578532, ss1639167943, ss1682161976, ss1938433527, ss2029997052, ss2158569126, ss2629490911, ss2704266629, ss2969447731, ss3018478216, ss3352597456, ss3685163291, ss3743554010, ss3758871501, ss3788696232, ss3793580122, ss3798467582, ss3835766110, ss3841507962, ss3889491451, ss3939819176, ss5230477036, ss5438585337, ss5512263916, ss5663572816, ss5845947678, ss5958506010	NC_000020.10:62291829:C:T	NC_000020.11:63660476:C:T	(self)
103728238, 557010751, 39024328, 124381038, 369864165, 8743125077, ss2244248546, ss3028831905, ss3651056225, ss3707317242, ss3822024982, ss3847021787, ss3982646327, ss5094755220, ss5309443819, ss5501658426, ss5616202303, ss5790543934, ss5818201825, ss5853217770, ss5924167841	NC_000020.11:63660476:C:T	NC_000020.11:63660476:C:T	(self)
ss8413246, ss21770136	NT_011333.5:1028459:C:T	NC_000020.11:63660476:C:T	(self)
ss3866066, ss41388631, ss96207149	NT_011333.6:1028460:C:T	NC_000020.11:63660476: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 rs2738778

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

rs2738778