Name: rs2797225
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.

rs2797225

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:215745224 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.404549 (107080/264690, TOPMED)
T=0.411717 (57642/140004, GnomAD)
T=0.42472 (12001/28256, 14KJPN) (+ 17 more)
T=0.41959 (7926/18890, ALFA)
T=0.41718 (6992/16760, 8.3KJPN)
T=0.3869 (2478/6404, 1000G_30x)
T=0.3892 (1949/5008, 1000G)
T=0.4911 (2200/4480, Estonian)
T=0.4286 (1652/3854, ALSPAC)
T=0.4234 (1570/3708, TWINSUK)
T=0.4137 (1212/2930, KOREAN)
T=0.4290 (786/1832, Korea1K)
T=0.417 (416/998, GoNL)
A=0.500 (300/600, NorthernSweden)
T=0.500 (300/600, NorthernSweden)
A=0.359 (137/382, SGDP_PRJ)
T=0.421 (91/216, Qatari)
T=0.366 (79/216, Vietnamese)
A=0.23 (11/48, Siberian)
T=0.35 (14/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: USH2A : 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=0.58041	T=0.41959
European	Sub	14286	A=0.56671	T=0.43329
African	Sub	2946	A=0.6409	T=0.3591
African Others	Sub	114	A=0.614	T=0.386
African American	Sub	2832	A=0.6419	T=0.3581
Asian	Sub	112	A=0.652	T=0.348
East Asian	Sub	86	A=0.66	T=0.34
Other Asian	Sub	26	A=0.62	T=0.38
Latin American 1	Sub	146	A=0.568	T=0.432
Latin American 2	Sub	610	A=0.544	T=0.456
South Asian	Sub	98	A=0.67	T=0.33
Other	Sub	692	A=0.616	T=0.384

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	A=0.595451	T=0.404549
gnomAD - Genomes	Global	Study-wide	140004	A=0.588283	T=0.411717
gnomAD - Genomes	European	Sub	75844	A=0.57152	T=0.42848
gnomAD - Genomes	African	Sub	41926	A=0.63035	T=0.36965
gnomAD - Genomes	American	Sub	13634	A=0.52838	T=0.47162
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.6460	T=0.3540
gnomAD - Genomes	East Asian	Sub	3128	A=0.6330	T=0.3670
gnomAD - Genomes	Other	Sub	2150	A=0.5851	T=0.4149
14KJPN	JAPANESE	Study-wide	28256	A=0.57528	T=0.42472
Allele Frequency Aggregator	Total	Global	18890	A=0.58041	T=0.41959
Allele Frequency Aggregator	European	Sub	14286	A=0.56671	T=0.43329
Allele Frequency Aggregator	African	Sub	2946	A=0.6409	T=0.3591
Allele Frequency Aggregator	Other	Sub	692	A=0.616	T=0.384
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.544	T=0.456
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.568	T=0.432
Allele Frequency Aggregator	Asian	Sub	112	A=0.652	T=0.348
Allele Frequency Aggregator	South Asian	Sub	98	A=0.67	T=0.33
8.3KJPN	JAPANESE	Study-wide	16760	A=0.58282	T=0.41718
1000Genomes_30x	Global	Study-wide	6404	A=0.6131	T=0.3869
1000Genomes_30x	African	Sub	1786	A=0.6198	T=0.3802
1000Genomes_30x	Europe	Sub	1266	A=0.5798	T=0.4202
1000Genomes_30x	South Asian	Sub	1202	A=0.7188	T=0.2812
1000Genomes_30x	East Asian	Sub	1170	A=0.6162	T=0.3838
1000Genomes_30x	American	Sub	980	A=0.510	T=0.490
1000Genomes	Global	Study-wide	5008	A=0.6108	T=0.3892
1000Genomes	African	Sub	1322	A=0.6210	T=0.3790
1000Genomes	East Asian	Sub	1008	A=0.6032	T=0.3968
1000Genomes	Europe	Sub	1006	A=0.5736	T=0.4264
1000Genomes	South Asian	Sub	978	A=0.715	T=0.285
1000Genomes	American	Sub	694	A=0.510	T=0.490
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5089	T=0.4911
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5714	T=0.4286
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5766	T=0.4234
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5863	T=0.4137
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5710	T=0.4290
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.583	T=0.417
Northern Sweden	ACPOP	Study-wide	600	A=0.500	T=0.500
SGDP_PRJ	Global	Study-wide	382	A=0.359	T=0.641
Qatari	Global	Study-wide	216	A=0.579	T=0.421
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.634	T=0.366
Siberian	Global	Study-wide	48	A=0.23	T=0.77
The Danish reference pan genome	Danish	Study-wide	40	A=0.65	T=0.35

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.215745224A>T
GRCh37.p13 chr 1	NC_000001.10:g.215918566A>T
USH2A RefSeqGene	NG_009497.2:g.683225T>A

Gene: USH2A, usherin (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
USH2A transcript variant 2	NM_206933.4:c.11390-1889T… NM_206933.4:c.11390-1889T>A	N/A	Intron Variant
USH2A transcript variant 1	NM_007123.6:c.	N/A	Genic Downstream 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	A=	T
GRCh38.p14 chr 1	NC_000001.11:g.215745224=	NC_000001.11:g.215745224A>T
GRCh37.p13 chr 1	NC_000001.10:g.215918566=	NC_000001.10:g.215918566A>T
USH2A RefSeqGene	NG_009497.2:g.683225=	NG_009497.2:g.683225T>A
USH2A transcript variant 2	NM_206933.2:c.11390-1889=	NM_206933.2:c.11390-1889T>A
USH2A transcript variant 2	NM_206933.4:c.11390-1889=	NM_206933.4:c.11390-1889T>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#.

67 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3961453	Sep 28, 2001 (100)
2	CSHL-HAPMAP	ss16432876	Feb 27, 2004 (120)
3	SSAHASNP	ss20516521	Apr 05, 2004 (121)
4	ABI	ss43885065	Mar 13, 2006 (126)
5	BCMHGSC_JDW	ss87967911	Mar 23, 2008 (129)
6	HUMANGENOME_JCVI	ss99286628	Feb 04, 2009 (130)
7	BGI	ss102820582	Dec 01, 2009 (131)
8	1000GENOMES	ss108939122	Jan 23, 2009 (130)
9	ENSEMBL	ss131745755	Dec 01, 2009 (131)
10	ENSEMBL	ss138152921	Dec 01, 2009 (131)
11	GMI	ss156275295	Dec 01, 2009 (131)
12	BUSHMAN	ss199600680	Jul 04, 2010 (132)
13	1000GENOMES	ss210737850	Jul 14, 2010 (132)
14	1000GENOMES	ss218877362	Jul 14, 2010 (132)
15	1000GENOMES	ss230898619	Jul 14, 2010 (132)
16	1000GENOMES	ss238511762	Jul 15, 2010 (132)
17	BL	ss253820751	May 09, 2011 (134)
18	GMI	ss276213814	May 04, 2012 (137)
19	GMI	ss284227063	Apr 25, 2013 (138)
20	PJP	ss290732246	May 09, 2011 (134)
21	TISHKOFF	ss555134139	Apr 25, 2013 (138)
22	SSMP	ss648695389	Apr 25, 2013 (138)
23	EVA-GONL	ss976135958	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1068594844	Aug 21, 2014 (142)
25	1000GENOMES	ss1294619209	Aug 21, 2014 (142)
26	DDI	ss1426108686	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1574673519	Apr 01, 2015 (144)
28	EVA_DECODE	ss1585532224	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1602124079	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1645118112	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1795718705	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1919359849	Feb 12, 2016 (147)
33	GENOMED	ss1966970809	Jul 19, 2016 (147)
34	JJLAB	ss2020202710	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2148233608	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2170022684	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2624610572	Nov 08, 2017 (151)
38	GRF	ss2698227043	Nov 08, 2017 (151)
39	GNOMAD	ss2766126206	Nov 08, 2017 (151)
40	SWEGEN	ss2988437912	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3023860957	Nov 08, 2017 (151)
42	CSHL	ss3343907921	Nov 08, 2017 (151)
43	URBANLAB	ss3646885112	Oct 11, 2018 (152)
44	EGCUT_WGS	ss3656397827	Jul 12, 2019 (153)
45	EVA_DECODE	ss3688615205	Jul 12, 2019 (153)
46	ACPOP	ss3727856065	Jul 12, 2019 (153)
47	EVA	ss3747326099	Jul 12, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3800330269	Jul 12, 2019 (153)
49	EVA	ss3826639110	Apr 25, 2020 (154)
50	EVA	ss3836720190	Apr 25, 2020 (154)
51	EVA	ss3842131953	Apr 25, 2020 (154)
52	SGDP_PRJ	ss3850881044	Apr 25, 2020 (154)
53	KRGDB	ss3896195561	Apr 25, 2020 (154)
54	KOGIC	ss3946478679	Apr 25, 2020 (154)
55	TOPMED	ss4483297380	Apr 25, 2021 (155)
56	TOMMO_GENOMICS	ss5148397989	Apr 25, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5245769864	Oct 12, 2022 (156)
58	HUGCELL_USP	ss5446209063	Oct 12, 2022 (156)
59	EVA	ss5506183127	Oct 12, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5519852866	Oct 12, 2022 (156)
61	SANFORD_IMAGENETICS	ss5627432767	Oct 12, 2022 (156)
62	TOMMO_GENOMICS	ss5676150005	Oct 12, 2022 (156)
63	YY_MCH	ss5801630984	Oct 12, 2022 (156)
64	EVA	ss5833250526	Oct 12, 2022 (156)
65	EVA	ss5849280957	Oct 12, 2022 (156)
66	EVA	ss5911944752	Oct 12, 2022 (156)
67	EVA	ss5939269523	Oct 12, 2022 (156)
68	1000Genomes	NC_000001.10 - 215918566	Oct 11, 2018 (152)
69	1000Genomes_30x	NC_000001.11 - 215745224	Oct 12, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 215918566	Oct 11, 2018 (152)
71	Genetic variation in the Estonian population	NC_000001.10 - 215918566	Oct 11, 2018 (152)
72	The Danish reference pan genome	NC_000001.10 - 215918566	Apr 25, 2020 (154)
73	gnomAD - Genomes	NC_000001.11 - 215745224	Apr 25, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000001.10 - 215918566	Apr 25, 2020 (154)
75	KOREAN population from KRGDB	NC_000001.10 - 215918566	Apr 25, 2020 (154)
76	Korean Genome Project	NC_000001.11 - 215745224	Apr 25, 2020 (154)
77	Northern Sweden	NC_000001.10 - 215918566	Jul 12, 2019 (153)
78	Qatari	NC_000001.10 - 215918566	Apr 25, 2020 (154)
79	SGDP_PRJ	NC_000001.10 - 215918566	Apr 25, 2020 (154)
80	Siberian	NC_000001.10 - 215918566	Apr 25, 2020 (154)
81	8.3KJPN	NC_000001.10 - 215918566	Apr 25, 2021 (155)
82	14KJPN	NC_000001.11 - 215745224	Oct 12, 2022 (156)
83	TopMed	NC_000001.11 - 215745224	Apr 25, 2021 (155)
84	UK 10K study - Twins	NC_000001.10 - 215918566	Oct 11, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000001.10 - 215918566	Jul 12, 2019 (153)
86	ALFA	NC_000001.11 - 215745224	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87967911, ss108939122, ss199600680, ss210737850, ss253820751, ss276213814, ss284227063, ss290732246, ss1585532224	NC_000001.9:213985188:A:T	NC_000001.11:215745223:A:T	(self)
5472688, 3021751, 2136075, 1880952, 1319367, 3372955, 1140930, 1401779, 2898024, 749962, 6367296, 3021751, 653384, ss218877362, ss230898619, ss238511762, ss555134139, ss648695389, ss976135958, ss1068594844, ss1294619209, ss1426108686, ss1574673519, ss1602124079, ss1645118112, ss1795718705, ss1919359849, ss1966970809, ss2020202710, ss2148233608, ss2624610572, ss2698227043, ss2766126206, ss2988437912, ss3343907921, ss3656397827, ss3727856065, ss3747326099, ss3826639110, ss3836720190, ss3850881044, ss3896195561, ss5148397989, ss5506183127, ss5627432767, ss5833250526, ss5939269523	NC_000001.10:215918565:A:T	NC_000001.11:215745223:A:T	(self)
7378801, 39353613, 2856680, 9987109, 46903715, 1745545762, ss2170022684, ss3023860957, ss3646885112, ss3688615205, ss3800330269, ss3842131953, ss3946478679, ss4483297380, ss5245769864, ss5446209063, ss5519852866, ss5676150005, ss5801630984, ss5849280957, ss5911944752	NC_000001.11:215745223:A:T	NC_000001.11:215745223:A:T	(self)
ss16432876, ss20516521	NT_021877.16:9354471:A:T	NC_000001.11:215745223:A:T	(self)
ss3961453, ss43885065, ss99286628, ss102820582, ss131745755, ss138152921, ss156275295	NT_167186.1:9436344:A:T	NC_000001.11:215745223: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 rs2797225

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

rs2797225