Name: rs688809
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.

rs688809

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:28757639 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.383373 (101475/264690, TOPMED)
A=0.378213 (52968/140048, GnomAD)
T=0.20950 (5920/28258, 14KJPN) (+ 15 more)
A=0.38497 (7272/18890, ALFA)
T=0.21080 (3533/16760, 8.3KJPN)
A=0.4799 (3073/6404, 1000G_30x)
A=0.4934 (2471/5008, 1000G)
A=0.4067 (1822/4480, Estonian)
A=0.4079 (1572/3854, ALSPAC)
A=0.3935 (1459/3708, TWINSUK)
T=0.2276 (667/2930, KOREAN)
A=0.416 (415/998, GoNL)
A=0.410 (246/600, NorthernSweden)
A=0.317 (114/360, SGDP_PRJ)
A=0.495 (107/216, Qatari)
T=0.215 (46/214, Vietnamese)
A=0.47 (19/40, GENOME_DK)
A=0.31 (11/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: YTHDF2 : 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	18890	A=0.38497	T=0.61503
European	Sub	14286	A=0.40011	T=0.59989
African	Sub	2946	A=0.2580	T=0.7420
African Others	Sub	114	A=0.237	T=0.763
African American	Sub	2832	A=0.2588	T=0.7412
Asian	Sub	112	A=0.812	T=0.188
East Asian	Sub	86	A=0.79	T=0.21
Other Asian	Sub	26	A=0.88	T=0.12
Latin American 1	Sub	146	A=0.288	T=0.712
Latin American 2	Sub	610	A=0.561	T=0.439
South Asian	Sub	98	A=0.49	T=0.51
Other	Sub	692	A=0.395	T=0.605

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
TopMed	Global	Study-wide	264690	A=0.383373	T=0.616627
gnomAD - Genomes	Global	Study-wide	140048	A=0.378213	T=0.621787
gnomAD - Genomes	European	Sub	75832	A=0.40623	T=0.59377
gnomAD - Genomes	African	Sub	41990	A=0.25716	T=0.74284
gnomAD - Genomes	American	Sub	13632	A=0.49076	T=0.50924
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.4367	T=0.5633
gnomAD - Genomes	East Asian	Sub	3122	A=0.7655	T=0.2345
gnomAD - Genomes	Other	Sub	2152	A=0.3880	T=0.6120
14KJPN	JAPANESE	Study-wide	28258	A=0.79050	T=0.20950
Allele Frequency Aggregator	Total	Global	18890	A=0.38497	T=0.61503
Allele Frequency Aggregator	European	Sub	14286	A=0.40011	T=0.59989
Allele Frequency Aggregator	African	Sub	2946	A=0.2580	T=0.7420
Allele Frequency Aggregator	Other	Sub	692	A=0.395	T=0.605
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.561	T=0.439
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.288	T=0.712
Allele Frequency Aggregator	Asian	Sub	112	A=0.812	T=0.188
Allele Frequency Aggregator	South Asian	Sub	98	A=0.49	T=0.51
8.3KJPN	JAPANESE	Study-wide	16760	A=0.78920	T=0.21080
1000Genomes_30x	Global	Study-wide	6404	A=0.4799	T=0.5201
1000Genomes_30x	African	Sub	1786	A=0.2144	T=0.7856
1000Genomes_30x	Europe	Sub	1266	A=0.3918	T=0.6082
1000Genomes_30x	South Asian	Sub	1202	A=0.6148	T=0.3852
1000Genomes_30x	East Asian	Sub	1170	A=0.7838	T=0.2162
1000Genomes_30x	American	Sub	980	A=0.549	T=0.451
1000Genomes	Global	Study-wide	5008	A=0.4934	T=0.5066
1000Genomes	African	Sub	1322	A=0.2186	T=0.7814
1000Genomes	East Asian	Sub	1008	A=0.7897	T=0.2103
1000Genomes	Europe	Sub	1006	A=0.3887	T=0.6113
1000Genomes	South Asian	Sub	978	A=0.630	T=0.370
1000Genomes	American	Sub	694	A=0.546	T=0.454
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.4067	T=0.5933
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.4079	T=0.5921
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3935	T=0.6065
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.7724	T=0.2276
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.416	T=0.584
Northern Sweden	ACPOP	Study-wide	600	A=0.410	T=0.590
SGDP_PRJ	Global	Study-wide	360	A=0.317	G=0.003, T=0.681
Qatari	Global	Study-wide	216	A=0.495	T=0.505
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.785	T=0.215
The Danish reference pan genome	Danish	Study-wide	40	A=0.47	T=0.53
Siberian	Global	Study-wide	36	A=0.31	T=0.69

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.28757639A>G
GRCh38.p14 chr 1	NC_000001.11:g.28757639A>T
GRCh37.p13 chr 1	NC_000001.10:g.29084151A>G
GRCh37.p13 chr 1	NC_000001.10:g.29084151A>T
YTHDF2 RefSeqGene	NG_016746.1:g.26016A>G
YTHDF2 RefSeqGene	NG_016746.1:g.26016A>T

Gene: YTHDF2, YTH N6-methyladenosine RNA binding protein 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
YTHDF2 transcript variant 3	NM_001172828.2:c.1567-112… NM_001172828.2:c.1567-11290A>G	N/A	Intron Variant
YTHDF2 transcript variant 2	NM_001173128.2:c.1717-112… NM_001173128.2:c.1717-11290A>G	N/A	Intron Variant
YTHDF2 transcript variant 1	NM_016258.3:c.1717-11290A… NM_016258.3:c.1717-11290A>G	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	A=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.28757639=	NC_000001.11:g.28757639A>G	NC_000001.11:g.28757639A>T
GRCh37.p13 chr 1	NC_000001.10:g.29084151=	NC_000001.10:g.29084151A>G	NC_000001.10:g.29084151A>T
YTHDF2 RefSeqGene	NG_016746.1:g.26016=	NG_016746.1:g.26016A>G	NG_016746.1:g.26016A>T
YTHDF2 transcript variant 3	NM_001172828.1:c.1567-11290=	NM_001172828.1:c.1567-11290A>G	NM_001172828.1:c.1567-11290A>T
YTHDF2 transcript variant 3	NM_001172828.2:c.1567-11290=	NM_001172828.2:c.1567-11290A>G	NM_001172828.2:c.1567-11290A>T
YTHDF2 transcript variant 2	NM_001173128.1:c.1717-11290=	NM_001173128.1:c.1717-11290A>G	NM_001173128.1:c.1717-11290A>T
YTHDF2 transcript variant 2	NM_001173128.2:c.1717-11290=	NM_001173128.2:c.1717-11290A>G	NM_001173128.2:c.1717-11290A>T
YTHDF2 transcript variant 1	NM_016258.2:c.1717-11290=	NM_016258.2:c.1717-11290A>G	NM_016258.2:c.1717-11290A>T
YTHDF2 transcript variant 1	NM_016258.3:c.1717-11290=	NM_016258.3:c.1717-11290A>G	NM_016258.3:c.1717-11290A>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#.

75 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss862526	Aug 11, 2000 (83)
2	TSC-CSHL	ss3268000	Sep 28, 2001 (100)
3	BCM_SSAHASNP	ss9865328	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss11394279	Jul 11, 2003 (116)
5	SC_SNP	ss13003894	Dec 05, 2003 (119)
6	SC_SNP	ss15413581	Feb 27, 2004 (120)
7	HGSV	ss77242561	Dec 07, 2007 (129)
8	HGSV	ss78700985	Dec 07, 2007 (129)
9	HGSV	ss81828630	Dec 14, 2007 (130)
10	HGSV	ss82420330	Dec 14, 2007 (130)
11	BCMHGSC_JDW	ss87323248	Mar 23, 2008 (129)
12	1000GENOMES	ss108083570	Jan 22, 2009 (130)
13	1000GENOMES	ss110223109	Jan 24, 2009 (130)
14	ILLUMINA-UK	ss118586183	Feb 14, 2009 (130)
15	ENSEMBL	ss137861620	Dec 01, 2009 (131)
16	GMI	ss154805791	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss163215299	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss164022718	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss166286597	Jul 04, 2010 (132)
20	BUSHMAN	ss198219854	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205221904	Jul 04, 2010 (132)
22	1000GENOMES	ss218298766	Jul 14, 2010 (132)
23	1000GENOMES	ss230473134	Jul 14, 2010 (132)
24	1000GENOMES	ss238177939	Jul 15, 2010 (132)
25	GMI	ss275764435	May 04, 2012 (137)
26	GMI	ss284024523	Apr 25, 2013 (138)
27	PJP	ss290796087	May 09, 2011 (134)
28	TISHKOFF	ss553927181	Apr 25, 2013 (138)
29	SSMP	ss647661186	Apr 25, 2013 (138)
30	EVA-GONL	ss974981661	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1067757733	Aug 21, 2014 (142)
32	1000GENOMES	ss1290179839	Aug 21, 2014 (142)
33	DDI	ss1425756321	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1573959893	Apr 01, 2015 (144)
35	EVA_DECODE	ss1584341287	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1599800307	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1642794340	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1794108564	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1918193346	Feb 12, 2016 (147)
40	GENOMED	ss1966710749	Jul 19, 2016 (147)
41	JJLAB	ss2019607905	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2147615780	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2161023918	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2624320204	Nov 08, 2017 (151)
45	GRF	ss2697521318	Nov 08, 2017 (151)
46	GNOMAD	ss2753102505	Nov 08, 2017 (151)
47	SWEGEN	ss2986527333	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3023569008	Nov 08, 2017 (151)
49	CSHL	ss3343381341	Nov 08, 2017 (151)
50	EGCUT_WGS	ss3654590469	Jul 12, 2019 (153)
51	EVA_DECODE	ss3686419832	Jul 12, 2019 (153)
52	ACPOP	ss3726898007	Jul 12, 2019 (153)
53	EVA	ss3745982390	Jul 12, 2019 (153)
54	PACBIO	ss3783363585	Jul 12, 2019 (153)
55	PACBIO	ss3789030646	Jul 12, 2019 (153)
56	PACBIO	ss3793903203	Jul 12, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3799001803	Jul 12, 2019 (153)
58	EVA	ss3826088224	Apr 25, 2020 (154)
59	EVA	ss3836431609	Apr 25, 2020 (154)
60	EVA	ss3841836589	Apr 25, 2020 (154)
61	SGDP_PRJ	ss3848484334	Apr 25, 2020 (154)
62	KRGDB	ss3893419814	Apr 25, 2020 (154)
63	TOPMED	ss4443425334	Apr 27, 2021 (155)
64	TOMMO_GENOMICS	ss5143112182	Apr 27, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5241642359	Oct 13, 2022 (156)
66	HUGCELL_USP	ss5442775729	Oct 13, 2022 (156)
67	EVA	ss5505797832	Oct 13, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5513611958	Oct 13, 2022 (156)
69	SANFORD_IMAGENETICS	ss5625182502	Oct 13, 2022 (156)
70	TOMMO_GENOMICS	ss5667615326	Oct 13, 2022 (156)
71	YY_MCH	ss5800442167	Oct 13, 2022 (156)
72	EVA	ss5831719524	Oct 13, 2022 (156)
73	EVA	ss5848835509	Oct 13, 2022 (156)
74	EVA	ss5907541582	Oct 13, 2022 (156)
75	EVA	ss5936998666	Oct 13, 2022 (156)
76	1000Genomes	NC_000001.10 - 29084151	Oct 11, 2018 (152)
77	1000Genomes_30x	NC_000001.11 - 28757639	Oct 13, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 29084151	Oct 11, 2018 (152)
79	Genetic variation in the Estonian population	NC_000001.10 - 29084151	Oct 11, 2018 (152)
80	The Danish reference pan genome	NC_000001.10 - 29084151	Apr 25, 2020 (154)
81	gnomAD - Genomes	NC_000001.11 - 28757639	Apr 27, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000001.10 - 29084151	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000001.10 - 29084151	Apr 25, 2020 (154)
84	Northern Sweden	NC_000001.10 - 29084151	Jul 12, 2019 (153)
85	Qatari	NC_000001.10 - 29084151	Apr 25, 2020 (154)
86	SGDP_PRJ	NC_000001.10 - 29084151	Apr 25, 2020 (154)
87	Siberian	NC_000001.10 - 29084151	Apr 25, 2020 (154)
88	8.3KJPN	NC_000001.10 - 29084151	Apr 27, 2021 (155)
89	14KJPN	NC_000001.11 - 28757639	Oct 13, 2022 (156)
90	TopMed	NC_000001.11 - 28757639	Apr 27, 2021 (155)
91	UK 10K study - Twins	NC_000001.10 - 29084151	Oct 11, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000001.10 - 29084151	Jul 12, 2019 (153)
93	ALFA	NC_000001.11 - 28757639	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)
rs58143116	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
501314, ss3848484334	NC_000001.10:29084150:A:G	NC_000001.11:28757638:A:G	(self)
ss77242561, ss78700985, ss81828630, ss82420330	NC_000001.8:28904766:A:T	NC_000001.11:28757638:A:T	(self)
ss87323248, ss108083570, ss110223109, ss118586183, ss163215299, ss164022718, ss166286597, ss198219854, ss205221904, ss275764435, ss284024523, ss290796087, ss1584341287	NC_000001.9:28956737:A:T	NC_000001.11:28757638:A:T	(self)
873203, 465389, 328717, 1437866, 199620, 597208, 182872, 235276, 501314, 132134, 1081489, 465389, 95706, ss218298766, ss230473134, ss238177939, ss553927181, ss647661186, ss974981661, ss1067757733, ss1290179839, ss1425756321, ss1573959893, ss1599800307, ss1642794340, ss1794108564, ss1918193346, ss1966710749, ss2019607905, ss2147615780, ss2624320204, ss2697521318, ss2753102505, ss2986527333, ss3343381341, ss3654590469, ss3726898007, ss3745982390, ss3783363585, ss3789030646, ss3793903203, ss3826088224, ss3836431609, ss3848484334, ss3893419814, ss5143112182, ss5505797832, ss5625182502, ss5831719524, ss5936998666	NC_000001.10:29084150:A:T	NC_000001.11:28757638:A:T	(self)
1137893, 6159840, 1452430, 7031669, 16136834990, ss2161023918, ss3023569008, ss3686419832, ss3799001803, ss3841836589, ss4443425334, ss5241642359, ss5442775729, ss5513611958, ss5667615326, ss5800442167, ss5848835509, ss5907541582	NC_000001.11:28757638:A:T	NC_000001.11:28757638:A:T	(self)
ss9865328, ss11394279, ss13003894	NT_004538.14:277106:A:T	NC_000001.11:28757638:A:T	(self)
ss15413581	NT_004538.15:273456:A:T	NC_000001.11:28757638:A:T	(self)
ss862526, ss3268000, ss137861620, ss154805791	NT_004610.19:15764238:A:T	NC_000001.11:28757638:A: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 rs688809

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

rs688809