Name: rs147619484
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.

rs147619484

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:38286776 (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=0.103461 (27385/264690, TOPMED)
T=0.106561 (12101/113559, GnomAD_exome)
T=0.08849 (8119/91750, GnomAD) (+ 14 more)
T=0.07353 (1361/18510, ALFA)
T=0.09334 (1548/16585, 14KJPN)
T=0.10668 (1679/15739, ExAC)
T=0.09579 (1227/12809, 8.3KJPN)
T=0.08055 (817/10143, GO-ESP)
T=0.1293 (488/3775, 1000G)
T=0.0461 (171/3708, TWINSUK)
T=0.0810 (237/2926, KOREAN)
T=0.0505 (146/2889, ALSPAC)
T=0.052 (28/534, MGP)
T=0.083 (9/108, Qatari)
C=0.20 (16/82, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
C=0.0 (0/2, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: RPGR : Missense Variant
Publications: 2 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	18510	C=0.92647	T=0.07353
European	Sub	14142	C=0.95022	T=0.04978
African	Sub	2898	C=0.8475	T=0.1525
African Others	Sub	114	C=0.816	T=0.184
African American	Sub	2784	C=0.8488	T=0.1512
Asian	Sub	112	C=0.973	T=0.027
East Asian	Sub	86	C=0.97	T=0.03
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.952	T=0.048
Latin American 2	Sub	610	C=0.787	T=0.213
South Asian	Sub	98	C=0.95	T=0.05
Other	Sub	504	C=0.861	T=0.139

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=0.896539	T=0.103461
gnomAD - Exomes	Global	Study-wide	113559	C=0.893439	T=0.106561
gnomAD - Exomes	European	Sub	54708	C=0.94202	T=0.05798
gnomAD - Exomes	Asian	Sub	22405	C=0.87927	T=0.12073
gnomAD - Exomes	American	Sub	19541	C=0.77882	T=0.22118
gnomAD - Exomes	African	Sub	7529	C=0.8308	T=0.1692
gnomAD - Exomes	Ashkenazi Jewish	Sub	6081	C=0.9373	T=0.0627
gnomAD - Exomes	Other	Sub	3295	C=0.9250	T=0.0750
gnomAD - Genomes	Global	Study-wide	91750	C=0.91151	T=0.08849
gnomAD - Genomes	European	Sub	51639	C=0.94707	T=0.05293
gnomAD - Genomes	African	Sub	26746	C=0.84869	T=0.15131
gnomAD - Genomes	American	Sub	7656	C=0.8746	T=0.1254
gnomAD - Genomes	Ashkenazi Jewish	Sub	2320	C=0.9336	T=0.0664
gnomAD - Genomes	East Asian	Sub	2000	C=0.9370	T=0.0630
gnomAD - Genomes	Other	Sub	1389	C=0.9287	T=0.0713
Allele Frequency Aggregator	Total	Global	18510	C=0.92647	T=0.07353
Allele Frequency Aggregator	European	Sub	14142	C=0.95022	T=0.04978
Allele Frequency Aggregator	African	Sub	2898	C=0.8475	T=0.1525
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.787	T=0.213
Allele Frequency Aggregator	Other	Sub	504	C=0.861	T=0.139
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.952	T=0.048
Allele Frequency Aggregator	Asian	Sub	112	C=0.973	T=0.027
Allele Frequency Aggregator	South Asian	Sub	98	C=0.95	T=0.05
14KJPN	JAPANESE	Study-wide	16585	C=0.90666	T=0.09334
ExAC	Global	Study-wide	15739	C=0.89332	T=0.10668
ExAC	Europe	Sub	7695	C=0.9409	T=0.0591
ExAC	Asian	Sub	4797	C=0.8547	T=0.1453
ExAC	African	Sub	2697	C=0.8391	T=0.1609
ExAC	American	Sub	403	C=0.787	T=0.213
ExAC	Other	Sub	147	C=0.952	T=0.048
8.3KJPN	JAPANESE	Study-wide	12809	C=0.90421	T=0.09579
GO Exome Sequencing Project	Global	Study-wide	10143	C=0.91945	T=0.08055
GO Exome Sequencing Project	European American	Sub	6483	C=0.9536	T=0.0464
GO Exome Sequencing Project	African American	Sub	3660	C=0.8590	T=0.1410
1000Genomes	Global	Study-wide	3775	C=0.8707	T=0.1293
1000Genomes	African	Sub	1003	C=0.8325	T=0.1675
1000Genomes	Europe	Sub	766	C=0.931	T=0.069
1000Genomes	East Asian	Sub	764	C=0.932	T=0.068
1000Genomes	South Asian	Sub	718	C=0.838	T=0.162
1000Genomes	American	Sub	524	C=0.811	T=0.189
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9539	T=0.0461
KOREAN population from KRGDB	KOREAN	Study-wide	2926	C=0.9190	G=0.0000, T=0.0810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	C=0.9495	T=0.0505
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.948	T=0.052
Qatari	Global	Study-wide	108	C=0.917	T=0.083
SGDP_PRJ	Global	Study-wide	82	C=0.20	T=0.80
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
Siberian	Global	Study-wide	2	C=0.0	T=1.0

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 X	NC_000023.11:g.38286776C>G
GRCh38.p14 chr X	NC_000023.11:g.38286776C>T
GRCh37.p13 chr X	NC_000023.10:g.38146029C>G
GRCh37.p13 chr X	NC_000023.10:g.38146029C>T
RPGR RefSeqGene	NG_009553.1:g.45760G>C
RPGR RefSeqGene	NG_009553.1:g.45760G>A

Gene: RPGR, retinitis pigmentosa GTPase regulator (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RPGR transcript variant A	NM_000328.3:c.1905+318G>C	N/A	Intron Variant
RPGR transcript variant D	NM_001367245.1:c.1902+318… NM_001367245.1:c.1902+318G>C	N/A	Intron Variant
RPGR transcript variant E	NM_001367246.1:c.1719+318… NM_001367246.1:c.1719+318G>C	N/A	Intron Variant
RPGR transcript variant F	NM_001367247.1:c.1572+418… NM_001367247.1:c.1572+4183G>C	N/A	Intron Variant
RPGR transcript variant G	NM_001367248.1:c.1602+418… NM_001367248.1:c.1602+4183G>C	N/A	Intron Variant
RPGR transcript variant H	NM_001367249.1:c.1569+418… NM_001367249.1:c.1569+4183G>C	N/A	Intron Variant
RPGR transcript variant I	NM_001367250.1:c.1569+418… NM_001367250.1:c.1569+4183G>C	N/A	Intron Variant
RPGR transcript variant J	NM_001367251.1:c.1386+418… NM_001367251.1:c.1386+4183G>C	N/A	Intron Variant
RPGR transcript variant C	NM_001034853.2:c.2223G>C	E [GAG] > D [GAC]	Coding Sequence Variant
X-linked retinitis pigmentosa GTPase regulator isoform C	NP_001030025.1:p.Glu741Asp	E (Glu) > D (Asp)	Missense Variant
RPGR transcript variant C	NM_001034853.2:c.2223G>A	E [GAG] > E [GAA]	Coding Sequence Variant
X-linked retinitis pigmentosa GTPase regulator isoform C	NP_001030025.1:p.Glu741=	E (Glu) > E (Glu)	Synonymous Variant
RPGR transcript variant K	NR_159803.1:n.	N/A	Intron Variant
RPGR transcript variant L	NR_159804.1:n.	N/A	Intron Variant
RPGR transcript variant M	NR_159805.1:n.	N/A	Intron Variant
RPGR transcript variant N	NR_159806.1:n.	N/A	Intron Variant
RPGR transcript variant O	NR_159807.1:n.	N/A	Intron Variant
RPGR transcript variant P	NR_159808.1:n.	N/A	Intron Variant
RPGR transcript variant X1	XM_047442329.1:c.2520+318… XM_047442329.1:c.2520+318G>C	N/A	Intron Variant
RPGR transcript variant X2	XM_047442330.1:c.2517+318… XM_047442330.1:c.2517+318G>C	N/A	Intron Variant
RPGR transcript variant X3	XM_047442331.1:c.1125+318… XM_047442331.1:c.1125+318G>C	N/A	Intron Variant
RPGR transcript variant X4	XR_007068198.1:n.	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.

Allele: T (allele ID: 257821 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000245344.3	not specified	Benign
RCV001682998.1	not provided	Benign
RCV002057421.3	Primary ciliary dyskinesia	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	C=	G	T
GRCh38.p14 chr X	NC_000023.11:g.38286776=	NC_000023.11:g.38286776C>G	NC_000023.11:g.38286776C>T
GRCh37.p13 chr X	NC_000023.10:g.38146029=	NC_000023.10:g.38146029C>G	NC_000023.10:g.38146029C>T
RPGR RefSeqGene	NG_009553.1:g.45760=	NG_009553.1:g.45760G>C	NG_009553.1:g.45760G>A
RPGR transcript variant C	NM_001034853.2:c.2223=	NM_001034853.2:c.2223G>C	NM_001034853.2:c.2223G>A
RPGR transcript variant C	NM_001034853.1:c.2223=	NM_001034853.1:c.2223G>C	NM_001034853.1:c.2223G>A
X-linked retinitis pigmentosa GTPase regulator isoform C	NP_001030025.1:p.Glu741=	NP_001030025.1:p.Glu741Asp	NP_001030025.1:p.Glu741=
RPGR transcript variant A	NM_000328.2:c.1905+318=	NM_000328.2:c.1905+318G>C	NM_000328.2:c.1905+318G>A
RPGR transcript variant A	NM_000328.3:c.1905+318=	NM_000328.3:c.1905+318G>C	NM_000328.3:c.1905+318G>A
RPGR transcript variant D	NM_001367245.1:c.1902+318=	NM_001367245.1:c.1902+318G>C	NM_001367245.1:c.1902+318G>A
RPGR transcript variant E	NM_001367246.1:c.1719+318=	NM_001367246.1:c.1719+318G>C	NM_001367246.1:c.1719+318G>A
RPGR transcript variant F	NM_001367247.1:c.1572+4183=	NM_001367247.1:c.1572+4183G>C	NM_001367247.1:c.1572+4183G>A
RPGR transcript variant G	NM_001367248.1:c.1602+4183=	NM_001367248.1:c.1602+4183G>C	NM_001367248.1:c.1602+4183G>A
RPGR transcript variant H	NM_001367249.1:c.1569+4183=	NM_001367249.1:c.1569+4183G>C	NM_001367249.1:c.1569+4183G>A
RPGR transcript variant I	NM_001367250.1:c.1569+4183=	NM_001367250.1:c.1569+4183G>C	NM_001367250.1:c.1569+4183G>A
RPGR transcript variant J	NM_001367251.1:c.1386+4183=	NM_001367251.1:c.1386+4183G>C	NM_001367251.1:c.1386+4183G>A
RPGR transcript variant X2	XM_005272633.1:c.1572+4183=	XM_005272633.1:c.1572+4183G>C	XM_005272633.1:c.1572+4183G>A
RPGR transcript variant X2	XM_005272634.1:c.*37+4183=	XM_005272634.1:c.*37+4183G>C	XM_005272634.1:c.*37+4183G>A
RPGR transcript variant X1	XM_047442329.1:c.2520+318=	XM_047442329.1:c.2520+318G>C	XM_047442329.1:c.2520+318G>A
RPGR transcript variant X2	XM_047442330.1:c.2517+318=	XM_047442330.1:c.2517+318G>C	XM_047442330.1:c.2517+318G>A
RPGR transcript variant X3	XM_047442331.1:c.1125+318=	XM_047442331.1:c.1125+318G>C	XM_047442331.1:c.1125+318G>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#.

43 SubSNP, 17 Frequency, 3 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss283734394	May 04, 2012 (137)
2	NHLBI-ESP	ss342551991	May 09, 2011 (134)
3	1000GENOMES	ss466450592	Sep 17, 2011 (135)
4	TISHKOFF	ss566837993	Apr 25, 2013 (138)
5	SSMP	ss662771223	Apr 25, 2013 (138)
6	WARNICH_LAB	ss678455838	Apr 25, 2013 (138)
7	JMKIDD_LAB	ss1082881098	Aug 21, 2014 (142)
8	DDI	ss1432030177	Apr 01, 2015 (144)
9	1000GENOMES	ss1554132400	Apr 01, 2015 (144)
10	EVA_GENOME_DK	ss1583373489	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1640625142	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1683619175	Apr 01, 2015 (144)
13	EVA_EXAC	ss1694491876	Apr 01, 2015 (144)
14	EVA_MGP	ss1711579861	Apr 01, 2015 (144)
15	WEILL_CORNELL_DGM	ss1939281795	Feb 12, 2016 (147)
16	ILLUMINA	ss1958188543	Feb 12, 2016 (147)
17	USC_VALOUEV	ss2159020921	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2316829034	Dec 20, 2016 (150)
19	GRF	ss2710144888	Nov 08, 2017 (151)
20	GNOMAD	ss2745358896	Nov 08, 2017 (151)
21	GNOMAD	ss2746092451	Nov 08, 2017 (151)
22	GNOMAD	ss2978038175	Nov 08, 2017 (151)
23	SWEGEN	ss3019854464	Nov 08, 2017 (151)
24	ILLUMINA	ss3023002251	Nov 08, 2017 (151)
25	CSHL	ss3352929262	Nov 08, 2017 (151)
26	OMUKHERJEE_ADBS	ss3646571860	Oct 12, 2018 (152)
27	ILLUMINA	ss3653560726	Oct 12, 2018 (152)
28	EVA	ss3770084113	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3822921308	Jul 13, 2019 (153)
30	EVA	ss3825480175	Apr 27, 2020 (154)
31	EVA	ss3836147495	Apr 27, 2020 (154)
32	SGDP_PRJ	ss3891289997	Apr 27, 2020 (154)
33	KRGDB	ss3941678277	Apr 27, 2020 (154)
34	TOPMED	ss5120405910	Apr 27, 2021 (155)
35	TOMMO_GENOMICS	ss5234151007	Apr 27, 2021 (155)
36	EVA	ss5237677157	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5312300332	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5665117158	Oct 16, 2022 (156)
39	TOMMO_GENOMICS	ss5795761878	Oct 16, 2022 (156)
40	EVA	ss5800238472	Oct 16, 2022 (156)
41	YY_MCH	ss5818994331	Oct 16, 2022 (156)
42	EVA	ss5857062448	Oct 16, 2022 (156)
43	EVA	ss5978109331	Oct 16, 2022 (156)
44	1000Genomes	NC_000023.10 - 38146029	Oct 12, 2018 (152)
45	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 38146029	Oct 12, 2018 (152)
46	ExAC	NC_000023.10 - 38146029	Oct 12, 2018 (152)
47	The Danish reference pan genome	NC_000023.10 - 38146029	Apr 27, 2020 (154)
48	gnomAD - Genomes	NC_000023.11 - 38286776	Apr 27, 2021 (155)
49	gnomAD - Exomes	NC_000023.10 - 38146029	Jul 13, 2019 (153)
50	GO Exome Sequencing Project	NC_000023.10 - 38146029	Oct 12, 2018 (152)
51	KOREAN population from KRGDB	NC_000023.10 - 38146029	Apr 27, 2020 (154)
52	Medical Genome Project healthy controls from Spanish population	NC_000023.10 - 38146029	Apr 27, 2020 (154)
53	Qatari	NC_000023.10 - 38146029	Apr 27, 2020 (154)
54	SGDP_PRJ	NC_000023.10 - 38146029	Apr 27, 2020 (154)
55	Siberian	NC_000023.10 - 38146029	Apr 27, 2020 (154)
56	8.3KJPN	NC_000023.10 - 38146029	Apr 27, 2021 (155)
57	14KJPN	NC_000023.11 - 38286776	Oct 16, 2022 (156)
58	TopMed	NC_000023.11 - 38286776	Apr 27, 2021 (155)
59	UK 10K study - Twins	NC_000023.10 - 38146029	Oct 12, 2018 (152)
60	ALFA	NC_000023.11 - 38286776	Apr 27, 2021 (155)
61	ClinVar	RCV000245344.3	Oct 16, 2022 (156)
62	ClinVar	RCV001682998.1	Oct 16, 2022 (156)
63	ClinVar	RCV002057421.3	Oct 16, 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
48855671, ss3941678277	NC_000023.10:38146028:C:G	NC_000023.11:38286775:C:G	(self)
ss283734394	NC_000023.9:38030972:C:T	NC_000023.11:38286775:C:T	(self)
82110235, 45343135, 9991691, 9538426, 14695136, 1936970, 48855671, 695621, 21323717, 43306977, 11537275, 92120314, 45343135, ss342551991, ss466450592, ss566837993, ss662771223, ss678455838, ss1082881098, ss1432030177, ss1554132400, ss1583373489, ss1640625142, ss1683619175, ss1694491876, ss1711579861, ss1939281795, ss1958188543, ss2159020921, ss2710144888, ss2745358896, ss2746092451, ss2978038175, ss3019854464, ss3023002251, ss3352929262, ss3646571860, ss3653560726, ss3770084113, ss3825480175, ss3836147495, ss3891289997, ss3941678277, ss5234151007, ss5665117158, ss5800238472, ss5978109331	NC_000023.10:38146028:C:T	NC_000023.11:38286775:C:T	(self)
RCV000245344.3, RCV001682998.1, RCV002057421.3, 578867832, 129598982, 684012267, 4977603151, ss2316829034, ss3822921308, ss5120405910, ss5237677157, ss5312300332, ss5795761878, ss5818994331, ss5857062448	NC_000023.11:38286775:C:T	NC_000023.11:38286775:C:T	(self)

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

2 citations for rs147619484

PMID	Title	Author	Year	Journal
24033266	A systematic approach to assessing the clinical significance of genetic variants.	Duzkale H et al.	2013	Clinical genetics
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S et al.	2015	Genetics in medicine

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

rs147619484