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dbSNP Short Genetic Variations

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 Aliases 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.

rs41303285

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:215741409 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.01582 (3977/251428, GnomAD_exome)
T=0.01175 (1475/125568, TOPMED)
T=0.01732 (2102/121392, ExAC) (+ 8 more)
T=0.0041 (324/78694, PAGE_STUDY)
T=0.0142 (444/31334, GnomAD)
T=0.0165 (215/13006, GO-ESP)
T=0.006 (31/5008, 1000G)
T=0.016 (71/4480, Estonian)
T=0.024 (92/3854, ALSPAC)
T=0.024 (88/3708, TWINSUK)
T=0.05 (32/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
USH2A : Missense Variant
Publications
3 citations
Genomic View
See rs on genome
Help

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.p12 chr 1 NC_000001.11:g.215741409G>T
GRCh37.p13 chr 1 NC_000001.10:g.215914751G>T
USH2A RefSeqGene NG_009497.1:g.686988C>A
Gene: USH2A, usherin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
USH2A transcript variant 1 NM_007123.5:c. N/A Genic Downstream Transcript Variant
USH2A transcript variant 2 NM_206933.3:c.11677C>A P [CCA] > T [ACA] Coding Sequence Variant
usherin isoform B precursor NP_996816.2:p.Pro3893Thr P (Pro) > T (Thr) Missense Variant
Help

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.

Allele: T (allele ID: 57542 )
ClinVar Accession Disease Names Clinical Significance
RCV000041701.3 not specified Benign
Help

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 - Exomes Global Study-wide 251428 G=0.98418 T=0.01582
gnomAD - Exomes European Sub 135358 G=0.97590 T=0.02410
gnomAD - Exomes Asian Sub 49008 G=0.9915 T=0.0085
gnomAD - Exomes American Sub 34592 G=0.9965 T=0.0035
gnomAD - Exomes African Sub 16256 G=0.9967 T=0.0033
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=0.9965 T=0.0035
gnomAD - Exomes Other Sub 6136 G=0.986 T=0.014
TopMed Global Study-wide 125568 G=0.98825 T=0.01175
ExAC Global Study-wide 121392 G=0.98268 T=0.01732
ExAC Europe Sub 73342 G=0.9758 T=0.0242
ExAC Asian Sub 25166 G=0.9910 T=0.0090
ExAC American Sub 11574 G=0.9959 T=0.0041
ExAC African Sub 10402 G=0.9961 T=0.0039
ExAC Other Sub 908 G=0.98 T=0.02
The PAGE Study Global Study-wide 78694 G=0.9959 T=0.0041
The PAGE Study AfricanAmerican Sub 32512 G=0.9954 T=0.0046
The PAGE Study Mexican Sub 10808 G=0.9956 T=0.0044
The PAGE Study Asian Sub 8316 G=1.000 T=0.000
The PAGE Study PuertoRican Sub 7918 G=0.996 T=0.004
The PAGE Study NativeHawaiian Sub 4534 G=0.994 T=0.006
The PAGE Study Cuban Sub 4230 G=0.994 T=0.006
The PAGE Study Dominican Sub 3828 G=0.996 T=0.004
The PAGE Study CentralAmerican Sub 2450 G=0.998 T=0.002
The PAGE Study SouthAmerican Sub 1982 G=0.998 T=0.002
The PAGE Study NativeAmerican Sub 1260 G=0.989 T=0.011
The PAGE Study SouthAsian Sub 856 G=0.99 T=0.01
gnomAD - Genomes Global Study-wide 31334 G=0.9858 T=0.0142
gnomAD - Genomes European Sub 18856 G=0.9798 T=0.0202
gnomAD - Genomes African Sub 8702 G=0.996 T=0.004
gnomAD - Genomes East Asian Sub 1556 G=1.000 T=0.000
gnomAD - Genomes Other Sub 1082 G=0.976 T=0.024
gnomAD - Genomes American Sub 848 G=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.99 T=0.01
GO Exome Sequencing Project Global Study-wide 13006 G=0.9835 T=0.0165
GO Exome Sequencing Project European American Sub 8600 G=0.978 T=0.022
GO Exome Sequencing Project African American Sub 4406 G=0.995 T=0.005
1000Genomes Global Study-wide 5008 G=0.994 T=0.006
1000Genomes African Sub 1322 G=1.000 T=0.000
1000Genomes East Asian Sub 1008 G=1.000 T=0.000
1000Genomes Europe Sub 1006 G=0.981 T=0.019
1000Genomes South Asian Sub 978 G=0.99 T=0.01
1000Genomes American Sub 694 G=0.99 T=0.01
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.984 T=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.976 T=0.024
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.976 T=0.024
Northern Sweden ACPOP Study-wide 600 G=0.95 T=0.05
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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= T Note
GRCh38.p12 chr 1 NC_000001.11:g.215741409= NC_000001.11:g.21574140...

NC_000001.11:g.215741409G>T

GRCh37.p13 chr 1 NC_000001.10:g.215914751= NC_000001.10:g.21591475...

NC_000001.10:g.215914751G>T

USH2A RefSeqGene NG_009497.1:g.686988= NG_009497.1:g.686988C>A
USH2A transcript variant 2 NM_206933.3:c.11677= NM_206933.3:c.11677C>A
USH2A transcript variant 2 NM_206933.2:c.11677= NM_206933.2:c.11677C>A
usherin isoform B precursor NP_996816.2:p.Pro3893= NP_996816.2:p.Pro3893Thr
Help

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, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss61705399 Oct 18, 2006 (127)
2 CGM_KYOTO ss76872117 Dec 07, 2007 (129)
3 ILLUMINA ss161045238 Dec 01, 2009 (131)
4 1000GENOMES ss230898606 Jul 14, 2010 (132)
5 LMM-PCPGM ss244317216 Jun 15, 2010 (132)
6 NHLBI-ESP ss342030123 May 09, 2011 (134)
7 ILLUMINA ss479433450 Sep 08, 2015 (146)
8 ILLUMINA ss482225987 May 04, 2012 (137)
9 ILLUMINA ss483869713 May 04, 2012 (137)
10 1000GENOMES ss489791964 May 04, 2012 (137)
11 EXOME_CHIP ss491310627 May 04, 2012 (137)
12 CLINSEQ_SNP ss491615236 May 04, 2012 (137)
13 ILLUMINA ss536065009 Sep 08, 2015 (146)
14 ILLUMINA ss779519011 Sep 08, 2015 (146)
15 ILLUMINA ss780748172 Sep 08, 2015 (146)
16 ILLUMINA ss782378416 Sep 08, 2015 (146)
17 ILLUMINA ss783426046 Sep 08, 2015 (146)
18 ILLUMINA ss834989468 Sep 08, 2015 (146)
19 EVA-GONL ss976135924 Aug 21, 2014 (142)
20 1000GENOMES ss1294619089 Aug 21, 2014 (142)
21 HAMMER_LAB ss1397272132 Sep 08, 2015 (146)
22 EVA_GENOME_DK ss1574673502 Apr 01, 2015 (144)
23 EVA_FINRISK ss1584015094 Apr 01, 2015 (144)
24 EVA_DECODE ss1585532194 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1602124013 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1645118046 Apr 01, 2015 (144)
27 EVA_EXAC ss1686055102 Apr 01, 2015 (144)
28 EVA_MGP ss1710943572 Apr 01, 2015 (144)
29 ILLUMINA ss1751898071 Sep 08, 2015 (146)
30 ILLUMINA ss1917742310 Feb 12, 2016 (147)
31 ILLUMINA ss1946023180 Feb 12, 2016 (147)
32 ILLUMINA ss1958356718 Feb 12, 2016 (147)
33 JJLAB ss2020202690 Sep 14, 2016 (149)
34 HUMAN_LONGEVITY ss2170022456 Dec 20, 2016 (150)
35 TOPMED ss2332639524 Dec 20, 2016 (150)
36 ILLUMINA ss2632628409 Nov 08, 2017 (151)
37 GNOMAD ss2732274814 Nov 08, 2017 (151)
38 GNOMAD ss2746561951 Nov 08, 2017 (151)
39 GNOMAD ss2766125910 Nov 08, 2017 (151)
40 AFFY ss2984894186 Nov 08, 2017 (151)
41 SWEGEN ss2988437846 Nov 08, 2017 (151)
42 ILLUMINA ss3021179561 Nov 08, 2017 (151)
43 TOPMED ss3103194330 Nov 08, 2017 (151)
44 ILLUMINA ss3626306959 Oct 11, 2018 (152)
45 ILLUMINA ss3626306960 Oct 11, 2018 (152)
46 ILLUMINA ss3630658336 Oct 11, 2018 (152)
47 ILLUMINA ss3634372559 Oct 11, 2018 (152)
48 ILLUMINA ss3636051406 Oct 11, 2018 (152)
49 ILLUMINA ss3640079912 Oct 11, 2018 (152)
50 ILLUMINA ss3644519179 Oct 11, 2018 (152)
51 ILLUMINA ss3651524745 Oct 11, 2018 (152)
52 ILLUMINA ss3653663963 Oct 11, 2018 (152)
53 EGCUT_WGS ss3656397781 Jul 12, 2019 (153)
54 ILLUMINA ss3725105073 Jul 12, 2019 (153)
55 ACPOP ss3727856024 Jul 12, 2019 (153)
56 ILLUMINA ss3744360028 Jul 12, 2019 (153)
57 ILLUMINA ss3744673430 Jul 12, 2019 (153)
58 PAGE_CC ss3770871532 Jul 12, 2019 (153)
59 ILLUMINA ss3772174327 Jul 12, 2019 (153)
60 KHV_HUMAN_GENOMES ss3800330227 Jul 12, 2019 (153)
61 1000Genomes NC_000001.10 - 215914751 Oct 11, 2018 (152)
62 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 215914751 Oct 11, 2018 (152)
63 Genetic variation in the Estonian population NC_000001.10 - 215914751 Oct 11, 2018 (152)
64 ExAC NC_000001.10 - 215914751 Oct 11, 2018 (152)
65 gnomAD - Genomes NC_000001.10 - 215914751 Jul 12, 2019 (153)
66 gnomAD - Exomes NC_000001.10 - 215914751 Jul 12, 2019 (153)
67 GO Exome Sequencing Project NC_000001.10 - 215914751 Oct 11, 2018 (152)
68 Northern Sweden NC_000001.10 - 215914751 Jul 12, 2019 (153)
69 The PAGE Study NC_000001.11 - 215741409 Jul 12, 2019 (153)
70 TopMed NC_000001.11 - 215741409 Oct 11, 2018 (152)
71 UK 10K study - Twins NC_000001.10 - 215914751 Oct 11, 2018 (152)
72 ClinVar RCV000041701.3 Oct 11, 2018 (152)
Help

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)
rs386495617 Aug 06, 2014 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss482225987, ss491615236, ss1397272132, ss1585532194 NC_000001.9:213981373:G:T NC_000001.11:215741408:G:T (self)
5472566, 3021680, 2136029, 5291449, 14952089, 1310274, 174528, 1140889, 3021680, ss230898606, ss342030123, ss479433450, ss483869713, ss489791964, ss491310627, ss536065009, ss779519011, ss780748172, ss782378416, ss783426046, ss834989468, ss976135924, ss1294619089, ss1574673502, ss1584015094, ss1602124013, ss1645118046, ss1686055102, ss1710943572, ss1751898071, ss1917742310, ss1946023180, ss1958356718, ss2020202690, ss2332639524, ss2632628409, ss2732274814, ss2746561951, ss2766125910, ss2984894186, ss2988437846, ss3021179561, ss3626306959, ss3626306960, ss3630658336, ss3634372559, ss3636051406, ss3640079912, ss3644519179, ss3651524745, ss3653663963, ss3656397781, ss3727856024, ss3744360028, ss3744673430, ss3772174327 NC_000001.10:215914750:G:T NC_000001.11:215741408:G:T (self)
RCV000041701.3, 93001, 29469015, ss244317216, ss2170022456, ss3103194330, ss3725105073, ss3770871532, ss3800330227 NC_000001.11:215741408:G:T NC_000001.11:215741408:G:T (self)
ss61705399 NT_021877.17:9377857:G:T NC_000001.11:215741408:G:T (self)
ss76872117, ss161045238 NT_167186.1:9432529:G:T NC_000001.11:215741408:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs41303285
PMID Title Author Year Journal
17405132 Molecular and in silico analyses of the full-length isoform of usherin identify new pathogenic alleles in Usher type II patients. Baux D et al. 2007 Human mutation
18273898 Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II. Dreyer B et al. 2008 Human mutation
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics

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.

Software version is: 2.0.1.post308+0fe9b3b