Name: rs61752901
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.

rs61752901

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:68439059 (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: T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.005693 (1507/264690, TOPMED)
G=0.005274 (1325/251234, GnomAD_exome)
G=0.000775 (149/192292, ALFA) (+ 8 more)
G=0.002325 (326/140224, GnomAD)
G=0.004012 (486/121148, ExAC)
G=0.01104 (869/78694, PAGE_STUDY)
G=0.0084 (54/6404, 1000G_30x)
G=0.0078 (39/5008, 1000G)
G=0.002 (1/534, MGP)
T=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: RPE65 : Missense Variant
LOC124904198 : Intron Variant
Publications: 1 citation
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	208660	T=0.999267	G=0.000733
European	Sub	173458	T=0.999475	G=0.000525
African	Sub	9760	T=0.9989	G=0.0011
African Others	Sub	356	T=1.000	G=0.000
African American	Sub	9404	T=0.9988	G=0.0012
Asian	Sub	6336	T=0.9997	G=0.0003
East Asian	Sub	4492	T=0.9996	G=0.0004
Other Asian	Sub	1844	T=1.0000	G=0.0000
Latin American 1	Sub	796	T=0.989	G=0.011
Latin American 2	Sub	968	T=0.969	G=0.031
South Asian	Sub	280	T=1.000	G=0.000
Other	Sub	17062	T=0.99941	G=0.00059

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	T=0.994307	G=0.005693
gnomAD - Exomes	Global	Study-wide	251234	T=0.994726	G=0.005274
gnomAD - Exomes	European	Sub	135252	T=1.000000	G=0.000000
gnomAD - Exomes	Asian	Sub	48982	T=0.99998	G=0.00002
gnomAD - Exomes	American	Sub	34542	T=0.96277	G=0.03723
gnomAD - Exomes	African	Sub	16254	T=0.99969	G=0.00031
gnomAD - Exomes	Ashkenazi Jewish	Sub	10076	T=1.00000	G=0.00000
gnomAD - Exomes	Other	Sub	6128	T=0.9946	G=0.0054
Allele Frequency Aggregator	Total	Global	192292	T=0.999225	G=0.000775
Allele Frequency Aggregator	European	Sub	163346	T=0.999443	G=0.000557
Allele Frequency Aggregator	Other	Sub	15618	T=0.99942	G=0.00058
Allele Frequency Aggregator	Asian	Sub	6336	T=0.9997	G=0.0003
Allele Frequency Aggregator	African	Sub	4948	T=0.9984	G=0.0016
Allele Frequency Aggregator	Latin American 2	Sub	968	T=0.969	G=0.031
Allele Frequency Aggregator	Latin American 1	Sub	796	T=0.989	G=0.011
Allele Frequency Aggregator	South Asian	Sub	280	T=1.000	G=0.000
gnomAD - Genomes	Global	Study-wide	140224	T=0.997675	G=0.002325
gnomAD - Genomes	European	Sub	75948	T=0.99999	G=0.00001
gnomAD - Genomes	African	Sub	42020	T=0.99950	G=0.00050
gnomAD - Genomes	American	Sub	13646	T=0.97919	G=0.02081
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=1.0000	G=0.0000
gnomAD - Genomes	East Asian	Sub	3132	T=1.0000	G=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9907	G=0.0093
ExAC	Global	Study-wide	121148	T=0.995988	G=0.004012
ExAC	Europe	Sub	73240	T=0.99993	G=0.00007
ExAC	Asian	Sub	25110	T=0.99996	G=0.00004
ExAC	American	Sub	11528	T=0.95888	G=0.04112
ExAC	African	Sub	10362	T=0.99971	G=0.00029
ExAC	Other	Sub	908	T=0.997	G=0.003
The PAGE Study	Global	Study-wide	78694	T=0.98896	G=0.01104
The PAGE Study	AfricanAmerican	Sub	32514	T=0.99966	G=0.00034
The PAGE Study	Mexican	Sub	10808	T=0.96725	G=0.03275
The PAGE Study	Asian	Sub	8318	T=1.0000	G=0.0000
The PAGE Study	PuertoRican	Sub	7916	T=0.9666	G=0.0334
The PAGE Study	NativeHawaiian	Sub	4534	T=0.9993	G=0.0007
The PAGE Study	Cuban	Sub	4230	T=0.9943	G=0.0057
The PAGE Study	Dominican	Sub	3828	T=0.9872	G=0.0128
The PAGE Study	CentralAmerican	Sub	2448	T=0.9714	G=0.0286
The PAGE Study	SouthAmerican	Sub	1982	T=0.9581	G=0.0419
The PAGE Study	NativeAmerican	Sub	1260	T=0.9913	G=0.0087
The PAGE Study	SouthAsian	Sub	856	T=1.000	G=0.000
1000Genomes_30x	Global	Study-wide	6404	T=0.9916	G=0.0084
1000Genomes_30x	African	Sub	1786	T=1.0000	G=0.0000
1000Genomes_30x	Europe	Sub	1266	T=1.0000	G=0.0000
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	G=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	G=0.0009
1000Genomes_30x	American	Sub	980	T=0.946	G=0.054
1000Genomes	Global	Study-wide	5008	T=0.9922	G=0.0078
1000Genomes	African	Sub	1322	T=1.0000	G=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9990	G=0.0010
1000Genomes	Europe	Sub	1006	T=1.0000	G=0.0000
1000Genomes	South Asian	Sub	978	T=1.000	G=0.000
1000Genomes	American	Sub	694	T=0.945	G=0.055
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.998	G=0.002
SGDP_PRJ	Global	Study-wide	2	T=0.5	G=0.5

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.68439059T>G
GRCh37.p13 chr 1	NC_000001.10:g.68904742T>G
RPE65 RefSeqGene	NG_008472.2:g.15901A>C

Gene: RPE65, retinoid isomerohydrolase RPE65 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RPE65 transcript variant 1	NM_000329.3:c.881A>C	K [AAA] > T [ACA]	Coding Sequence Variant
retinoid isomerohydrolase isoform 1	NP_000320.1:p.Lys294Thr	K (Lys) > T (Thr)	Missense Variant

Gene: LOC124904198, uncharacterized LOC124904198 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124904198 transcript	XR_007066164.1: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.

Allele: G (allele ID: 98766 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000078655.10	not specified	Benign-Likely-Benign
RCV000085227.4	not provided	Not-Provided
RCV000552728.8	Leber congenital amaurosis 2,Retinitis pigmentosa 20	Benign-Likely-Benign
RCV001097019.3	Leber congenital amaurosis 2	Benign
RCV001097020.3	Retinitis pigmentosa	Benign
RCV001275283.2	Leber congenital amaurosis	Benign

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	T=	G
GRCh38.p14 chr 1	NC_000001.11:g.68439059=	NC_000001.11:g.68439059T>G
GRCh37.p13 chr 1	NC_000001.10:g.68904742=	NC_000001.10:g.68904742T>G
RPE65 RefSeqGene	NG_008472.2:g.15901=	NG_008472.2:g.15901A>C
RPE65 transcript variant 1	NM_000329.3:c.881=	NM_000329.3:c.881A>C
RPE65 transcript	NM_000329.2:c.881=	NM_000329.2:c.881A>C
RPE65 transcript variant 4	NM_001406857.1:c.605=	NM_001406857.1:c.605A>C
RPE65 transcript variant 2	NM_001406853.1:c.773=	NM_001406853.1:c.773A>C
RPE65 transcript variant 3	NM_001406856.1:c.605=	NM_001406856.1:c.605A>C
RPE65 transcript variant 5	NM_001406859.1:c.881=	NM_001406859.1:c.881A>C
retinoid isomerohydrolase isoform 1	NP_000320.1:p.Lys294=	NP_000320.1:p.Lys294Thr

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#.

50 SubSNP, 10 Frequency, 6 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss454124670	Sep 17, 2011 (135)
2	1000GENOMES	ss489747777	May 04, 2012 (137)
3	EXOME_CHIP	ss491295304	May 04, 2012 (137)
4	CLINSEQ_SNP	ss491596575	May 04, 2012 (137)
5	RISN-LSDB	ss562043722	Dec 21, 2012 (137)
6	ILLUMINA	ss780788917	Aug 21, 2014 (142)
7	ILLUMINA	ss783469667	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1067422371	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1067962697	Aug 21, 2014 (142)
10	1000GENOMES	ss1291265430	Aug 21, 2014 (142)
11	EVA_EXAC	ss1685594012	Apr 01, 2015 (144)
12	EVA_MGP	ss1710908727	Apr 01, 2015 (144)
13	ILLUMINA	ss1751930829	Sep 08, 2015 (146)
14	ILLUMINA	ss1917729994	Feb 12, 2016 (147)
15	ILLUMINA	ss1945998032	Feb 12, 2016 (147)
16	ILLUMINA	ss1958281605	Feb 12, 2016 (147)
17	JJLAB	ss2019750466	Sep 14, 2016 (149)
18	HUMAN_LONGEVITY	ss2163281348	Dec 20, 2016 (150)
19	GNOMAD	ss2731569613	Nov 08, 2017 (151)
20	GNOMAD	ss2746353051	Nov 08, 2017 (151)
21	GNOMAD	ss2756199186	Nov 08, 2017 (151)
22	AFFY	ss2984863804	Nov 08, 2017 (151)
23	ILLUMINA	ss3021096858	Nov 08, 2017 (151)
24	ILLUMINA	ss3626120116	Oct 11, 2018 (152)
25	ILLUMINA	ss3634329535	Oct 11, 2018 (152)
26	ILLUMINA	ss3640036896	Oct 11, 2018 (152)
27	ILLUMINA	ss3644493961	Oct 11, 2018 (152)
28	ILLUMINA	ss3651424803	Oct 11, 2018 (152)
29	ILLUMINA	ss3653635221	Oct 11, 2018 (152)
30	EVA_DECODE	ss3686955564	Jul 12, 2019 (153)
31	ILLUMINA	ss3725032859	Jul 12, 2019 (153)
32	ILLUMINA	ss3744346953	Jul 12, 2019 (153)
33	ILLUMINA	ss3744630519	Jul 12, 2019 (153)
34	EVA	ss3746319578	Jul 12, 2019 (153)
35	PAGE_CC	ss3770815825	Jul 12, 2019 (153)
36	ILLUMINA	ss3772131829	Jul 12, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3799326321	Jul 12, 2019 (153)
38	SGDP_PRJ	ss3849042304	Apr 25, 2020 (154)
39	EVA	ss3986123825	Apr 25, 2021 (155)
40	TOPMED	ss4453024566	Apr 25, 2021 (155)
41	EVA	ss5236870153	Apr 25, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5242592929	Oct 12, 2022 (156)
43	EVA	ss5319322869	Oct 12, 2022 (156)
44	HUGCELL_USP	ss5443624199	Oct 12, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5515031822	Oct 12, 2022 (156)
46	SANFORD_IMAGENETICS	ss5624208046	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5625714794	Oct 12, 2022 (156)
48	EVA	ss5908635080	Oct 12, 2022 (156)
49	EVA	ss5937554232	Oct 12, 2022 (156)
50	EVA	ss5979277284	Oct 12, 2022 (156)
51	1000Genomes	NC_000001.10 - 68904742	Oct 11, 2018 (152)
52	1000Genomes_30x	NC_000001.11 - 68439059	Oct 12, 2022 (156)
53	ExAC	NC_000001.10 - 68904742	Oct 11, 2018 (152)
54	gnomAD - Genomes	NC_000001.11 - 68439059	Apr 25, 2021 (155)
55	gnomAD - Exomes	NC_000001.10 - 68904742	Jul 12, 2019 (153)
56	Medical Genome Project healthy controls from Spanish population	NC_000001.10 - 68904742	Apr 25, 2020 (154)
57	The PAGE Study	NC_000001.11 - 68439059	Jul 12, 2019 (153)
58	SGDP_PRJ	NC_000001.10 - 68904742	Apr 25, 2020 (154)
59	TopMed	NC_000001.11 - 68439059	Apr 25, 2021 (155)
60	ALFA	NC_000001.11 - 68439059	Apr 25, 2021 (155)
61	ClinVar	RCV000078655.10	Oct 12, 2022 (156)
62	ClinVar	RCV000085227.4	Oct 12, 2022 (156)
63	ClinVar	RCV000552728.8	Oct 12, 2022 (156)
64	ClinVar	RCV001097019.3	Oct 12, 2022 (156)
65	ClinVar	RCV001097020.3	Oct 12, 2022 (156)
66	ClinVar	RCV001275283.2	Oct 12, 2022 (156)

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
ss491596575	NC_000001.9:68677329:T:G	NC_000001.11:68439058:T:G	(self)
1997283, 4794587, 589210, 25479, 1059284, ss454124670, ss489747777, ss491295304, ss780788917, ss783469667, ss1067422371, ss1067962697, ss1291265430, ss1685594012, ss1710908727, ss1751930829, ss1917729994, ss1945998032, ss1958281605, ss2019750466, ss2731569613, ss2746353051, ss2756199186, ss2984863804, ss3021096858, ss3626120116, ss3634329535, ss3640036896, ss3644493961, ss3651424803, ss3653635221, ss3744346953, ss3744630519, ss3746319578, ss3772131829, ss3849042304, ss3986123825, ss5319322869, ss5624208046, ss5625714794, ss5937554232, ss5979277284	NC_000001.10:68904741:T:G	NC_000001.11:68439058:T:G	(self)
RCV000078655.10, RCV000085227.4, RCV000552728.8, RCV001097019.3, RCV001097020.3, RCV001275283.2, 2557757, 14080962, 37294, 16630901, 5364783162, ss562043722, ss2163281348, ss3686955564, ss3725032859, ss3770815825, ss3799326321, ss4453024566, ss5236870153, ss5242592929, ss5443624199, ss5515031822, ss5908635080	NC_000001.11:68439058:T:G	NC_000001.11:68439058:T:G	(self)

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

1 citation for rs61752901

PMID	Title	Author	Year	Journal
23757202	Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.	Bean LJ et al.	2013	Human mutation

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

rs61752901