Name: rs7356969
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.

rs7356969

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:79525287 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.196426 (51992/264690, TOPMED)
A=0.173030 (24209/139912, GnomAD)
G=0.44646 (12616/28258, 14KJPN) (+ 15 more)
A=0.13272 (2507/18890, ALFA)
G=0.44481 (7455/16760, 8.3KJPN)
A=0.2898 (1856/6404, 1000G_30x)
A=0.2985 (1495/5008, 1000G)
A=0.1087 (487/4480, Estonian)
A=0.0739 (285/3854, ALSPAC)
A=0.0709 (263/3708, TWINSUK)
G=0.3816 (1118/2930, KOREAN)
G=0.4127 (756/1832, Korea1K)
A=0.064 (64/998, GoNL)
A=0.105 (63/600, NorthernSweden)
G=0.380 (105/276, SGDP_PRJ)
A=0.218 (47/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.46 (13/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LCA5 : Intron Variant
LOC124901348 : 2KB Upstream 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	G=0.86728	A=0.13272
European	Sub	14286	G=0.90942	A=0.09058
African	Sub	2946	G=0.7441	A=0.2559
African Others	Sub	114	G=0.702	A=0.298
African American	Sub	2832	G=0.7458	A=0.2542
Asian	Sub	112	G=0.402	A=0.598
East Asian	Sub	86	G=0.42	A=0.58
Other Asian	Sub	26	G=0.35	A=0.65
Latin American 1	Sub	146	G=0.836	A=0.164
Latin American 2	Sub	610	G=0.649	A=0.351
South Asian	Sub	98	G=0.81	A=0.19
Other	Sub	692	G=0.805	A=0.195

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	G=0.803574	A=0.196426
gnomAD - Genomes	Global	Study-wide	139912	G=0.826970	A=0.173030
gnomAD - Genomes	European	Sub	75824	G=0.90645	A=0.09355
gnomAD - Genomes	African	Sub	41884	G=0.74200	A=0.25800
gnomAD - Genomes	American	Sub	13612	G=0.73685	A=0.26315
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.8763	A=0.1237
gnomAD - Genomes	East Asian	Sub	3120	G=0.3955	A=0.6045
gnomAD - Genomes	Other	Sub	2150	G=0.7995	A=0.2005
14KJPN	JAPANESE	Study-wide	28258	G=0.44646	A=0.55354
Allele Frequency Aggregator	Total	Global	18890	G=0.86728	A=0.13272
Allele Frequency Aggregator	European	Sub	14286	G=0.90942	A=0.09058
Allele Frequency Aggregator	African	Sub	2946	G=0.7441	A=0.2559
Allele Frequency Aggregator	Other	Sub	692	G=0.805	A=0.195
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.649	A=0.351
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.836	A=0.164
Allele Frequency Aggregator	Asian	Sub	112	G=0.402	A=0.598
Allele Frequency Aggregator	South Asian	Sub	98	G=0.81	A=0.19
8.3KJPN	JAPANESE	Study-wide	16760	G=0.44481	A=0.55519
1000Genomes_30x	Global	Study-wide	6404	G=0.7102	A=0.2898
1000Genomes_30x	African	Sub	1786	G=0.7184	A=0.2816
1000Genomes_30x	Europe	Sub	1266	G=0.9163	A=0.0837
1000Genomes_30x	South Asian	Sub	1202	G=0.7587	A=0.2413
1000Genomes_30x	East Asian	Sub	1170	G=0.4291	A=0.5709
1000Genomes_30x	American	Sub	980	G=0.705	A=0.295
1000Genomes	Global	Study-wide	5008	G=0.7015	A=0.2985
1000Genomes	African	Sub	1322	G=0.7118	A=0.2882
1000Genomes	East Asian	Sub	1008	G=0.4306	A=0.5694
1000Genomes	Europe	Sub	1006	G=0.9145	A=0.0855
1000Genomes	South Asian	Sub	978	G=0.746	A=0.254
1000Genomes	American	Sub	694	G=0.703	A=0.297
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8913	A=0.1087
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9261	A=0.0739
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9291	A=0.0709
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3816	A=0.6184, C=0.0000, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4127	A=0.5873
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.936	A=0.064
Northern Sweden	ACPOP	Study-wide	600	G=0.895	A=0.105
SGDP_PRJ	Global	Study-wide	276	G=0.380	A=0.620
Qatari	Global	Study-wide	216	G=0.782	A=0.218
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
Siberian	Global	Study-wide	28	G=0.46	A=0.54

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 6	NC_000006.12:g.79525287G>A
GRCh38.p14 chr 6	NC_000006.12:g.79525287G>C
GRCh38.p14 chr 6	NC_000006.12:g.79525287G>T
GRCh37.p13 chr 6	NC_000006.11:g.80235004G>A
GRCh37.p13 chr 6	NC_000006.11:g.80235004G>C
GRCh37.p13 chr 6	NC_000006.11:g.80235004G>T
LCA5 RefSeqGene	NG_016011.1:g.17144C>T
LCA5 RefSeqGene	NG_016011.1:g.17144C>G
LCA5 RefSeqGene	NG_016011.1:g.17144C>A

Gene: LCA5, lebercilin LCA5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LCA5 transcript variant 2	NM_001122769.3:c.-191-620… NM_001122769.3:c.-191-6202C>T	N/A	Intron Variant
LCA5 transcript variant 1	NM_181714.4:c.-297-18C>T	N/A	Intron Variant
LCA5 transcript variant X1	XM_005248665.5:c.-191-620… XM_005248665.5:c.-191-6202C>T	N/A	Intron Variant
LCA5 transcript variant X2	XM_011535504.2:c.-297-18C… XM_011535504.2:c.-297-18C>T	N/A	Intron Variant
LCA5 transcript variant X3	XM_047418251.1:c.-191-620… XM_047418251.1:c.-191-6202C>T	N/A	Intron Variant

Gene: LOC124901348, uncharacterized LOC124901348 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124901348 transcript	XR_007059654.1:n.	N/A	Upstream 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	G=	A	C	T
GRCh38.p14 chr 6	NC_000006.12:g.79525287=	NC_000006.12:g.79525287G>A	NC_000006.12:g.79525287G>C	NC_000006.12:g.79525287G>T
GRCh37.p13 chr 6	NC_000006.11:g.80235004=	NC_000006.11:g.80235004G>A	NC_000006.11:g.80235004G>C	NC_000006.11:g.80235004G>T
LCA5 RefSeqGene	NG_016011.1:g.17144=	NG_016011.1:g.17144C>T	NG_016011.1:g.17144C>G	NG_016011.1:g.17144C>A
LCA5 transcript variant 2	NM_001122769.2:c.-191-6202=	NM_001122769.2:c.-191-6202C>T	NM_001122769.2:c.-191-6202C>G	NM_001122769.2:c.-191-6202C>A
LCA5 transcript variant 2	NM_001122769.3:c.-191-6202=	NM_001122769.3:c.-191-6202C>T	NM_001122769.3:c.-191-6202C>G	NM_001122769.3:c.-191-6202C>A
LCA5 transcript variant 1	NM_181714.3:c.-297-18=	NM_181714.3:c.-297-18C>T	NM_181714.3:c.-297-18C>G	NM_181714.3:c.-297-18C>A
LCA5 transcript variant 1	NM_181714.4:c.-297-18=	NM_181714.4:c.-297-18C>T	NM_181714.4:c.-297-18C>G	NM_181714.4:c.-297-18C>A
LCA5 transcript variant X2	XM_005248665.1:c.-191-6202=	XM_005248665.1:c.-191-6202C>T	XM_005248665.1:c.-191-6202C>G	XM_005248665.1:c.-191-6202C>A
LCA5 transcript variant X1	XM_005248665.5:c.-191-6202=	XM_005248665.5:c.-191-6202C>T	XM_005248665.5:c.-191-6202C>G	XM_005248665.5:c.-191-6202C>A
LCA5 transcript variant X2	XM_011535504.2:c.-297-18=	XM_011535504.2:c.-297-18C>T	XM_011535504.2:c.-297-18C>G	XM_011535504.2:c.-297-18C>A
LCA5 transcript variant X3	XM_047418251.1:c.-191-6202=	XM_047418251.1:c.-191-6202C>T	XM_047418251.1:c.-191-6202C>G	XM_047418251.1:c.-191-6202C>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#.

64 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss11121725	Jul 11, 2003 (116)
2	SC_SNP	ss12784388	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss20271221	Feb 27, 2004 (120)
4	ABI	ss42682067	Mar 14, 2006 (126)
5	HUMANGENOME_JCVI	ss98512711	Feb 04, 2009 (130)
6	BGI	ss106014614	Feb 04, 2009 (130)
7	ENSEMBL	ss144209379	Dec 01, 2009 (131)
8	GMI	ss157198808	Dec 01, 2009 (131)
9	BCM-HGSC-SUB	ss207674030	Jul 04, 2010 (132)
10	1000GENOMES	ss211870585	Jul 14, 2010 (132)
11	1000GENOMES	ss222493811	Jul 14, 2010 (132)
12	1000GENOMES	ss233551612	Jul 15, 2010 (132)
13	1000GENOMES	ss240592256	Jul 15, 2010 (132)
14	GMI	ss278886148	May 04, 2012 (137)
15	PJP	ss293645415	May 09, 2011 (134)
16	TISHKOFF	ss559317807	Apr 25, 2013 (138)
17	SSMP	ss653282086	Apr 25, 2013 (138)
18	EVA-GONL	ss983140351	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1073766060	Aug 21, 2014 (142)
20	1000GENOMES	ss1320912576	Aug 21, 2014 (142)
21	DDI	ss1430794101	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1581756874	Apr 01, 2015 (144)
23	EVA_DECODE	ss1592686279	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1615971644	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1658965677	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1804522364	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1926399003	Feb 12, 2016 (147)
28	GENOMED	ss1970445577	Jul 19, 2016 (147)
29	JJLAB	ss2023841923	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2152034188	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2285491463	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2626415821	Nov 08, 2017 (151)
33	GRF	ss2707647974	Nov 08, 2017 (151)
34	GNOMAD	ss2841192606	Nov 08, 2017 (151)
35	SWEGEN	ss2999401472	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3025714370	Nov 08, 2017 (151)
37	CSHL	ss3347070513	Nov 08, 2017 (151)
38	URBANLAB	ss3648396972	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3667275194	Jul 13, 2019 (153)
40	ACPOP	ss3733683203	Jul 13, 2019 (153)
41	EVA	ss3765255604	Jul 13, 2019 (153)
42	PACBIO	ss3785530285	Jul 13, 2019 (153)
43	PACBIO	ss3790873042	Jul 13, 2019 (153)
44	PACBIO	ss3795752130	Jul 13, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3808406031	Jul 13, 2019 (153)
46	EVA	ss3830026729	Apr 26, 2020 (154)
47	EVA	ss3838494751	Apr 26, 2020 (154)
48	EVA	ss3843942173	Apr 26, 2020 (154)
49	SGDP_PRJ	ss3864994621	Apr 26, 2020 (154)
50	KRGDB	ss3911873386	Apr 26, 2020 (154)
51	KOGIC	ss3959422119	Apr 26, 2020 (154)
52	TOPMED	ss4709789028	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5178387501	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5269145375	Oct 13, 2022 (156)
55	HUGCELL_USP	ss5466712368	Oct 13, 2022 (156)
56	EVA	ss5508578573	Oct 13, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5555440673	Oct 13, 2022 (156)
58	SANFORD_IMAGENETICS	ss5640803835	Oct 13, 2022 (156)
59	TOMMO_GENOMICS	ss5716825202	Oct 13, 2022 (156)
60	YY_MCH	ss5807656489	Oct 13, 2022 (156)
61	EVA	ss5842525458	Oct 13, 2022 (156)
62	EVA	ss5855436801	Oct 13, 2022 (156)
63	EVA	ss5884583122	Oct 13, 2022 (156)
64	EVA	ss5969301827	Oct 13, 2022 (156)
65	1000Genomes	NC_000006.11 - 80235004	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000006.12 - 79525287	Oct 13, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 80235004	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000006.11 - 80235004	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000006.11 - 80235004	Apr 26, 2020 (154)
70	gnomAD - Genomes	NC_000006.12 - 79525287	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000006.11 - 80235004	Apr 26, 2020 (154)
72	KOREAN population from KRGDB	NC_000006.11 - 80235004	Apr 26, 2020 (154)
73	Korean Genome Project	NC_000006.12 - 79525287	Apr 26, 2020 (154)
74	Northern Sweden	NC_000006.11 - 80235004	Jul 13, 2019 (153)
75	Qatari	NC_000006.11 - 80235004	Apr 26, 2020 (154)
76	SGDP_PRJ	NC_000006.11 - 80235004	Apr 26, 2020 (154)
77	Siberian	NC_000006.11 - 80235004	Apr 26, 2020 (154)
78	8.3KJPN	NC_000006.11 - 80235004	Apr 26, 2021 (155)
79	14KJPN	NC_000006.12 - 79525287	Oct 13, 2022 (156)
80	TopMed	NC_000006.12 - 79525287	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000006.11 - 80235004	Oct 12, 2018 (152)
82	ALFA	NC_000006.12 - 79525287	Apr 26, 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
ss207674030, ss211870585, ss278886148, ss293645415, ss1592686279	NC_000006.10:80291722:G:A	NC_000006.12:79525286:G:A	(self)
32729619, 18230856, 13013442, 7921813, 8123830, 19050780, 6968068, 8440933, 17011601, 4550542, 36356808, 18230856, ss222493811, ss233551612, ss240592256, ss559317807, ss653282086, ss983140351, ss1073766060, ss1320912576, ss1430794101, ss1581756874, ss1615971644, ss1658965677, ss1804522364, ss1926399003, ss1970445577, ss2023841923, ss2152034188, ss2626415821, ss2707647974, ss2841192606, ss2999401472, ss3347070513, ss3667275194, ss3733683203, ss3765255604, ss3785530285, ss3790873042, ss3795752130, ss3830026729, ss3838494751, ss3864994621, ss3911873386, ss5178387501, ss5508578573, ss5640803835, ss5842525458, ss5969301827	NC_000006.11:80235003:G:A	NC_000006.12:79525286:G:A	(self)
42966608, 230976687, 15800120, 50662306, 547166586, 14651701450, ss2285491463, ss3025714370, ss3648396972, ss3808406031, ss3843942173, ss3959422119, ss4709789028, ss5269145375, ss5466712368, ss5555440673, ss5716825202, ss5807656489, ss5855436801, ss5884583122	NC_000006.12:79525286:G:A	NC_000006.12:79525286:G:A	(self)
ss11121725, ss20271221	NT_007299.12:18055174:G:A	NC_000006.12:79525286:G:A	(self)
ss12784388, ss42682067, ss98512711, ss106014614, ss144209379, ss157198808	NT_007299.13:18354837:G:A	NC_000006.12:79525286:G:A	(self)
19050780, ss3911873386	NC_000006.11:80235003:G:C	NC_000006.12:79525286:G:C	(self)
19050780, ss3911873386	NC_000006.11:80235003:G:T	NC_000006.12:79525286:G: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 rs7356969

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

rs7356969