Name: rs598002
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.

rs598002

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:183128137 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.149469 (39563/264690, TOPMED)
C=0.133478 (18051/135236, GnomAD)
C=0.26651 (7530/28254, 14KJPN) (+ 10 more)
C=0.10669 (1849/17330, ALFA)
C=0.26319 (4411/16760, 8.3KJPN)
C=0.1971 (1262/6404, 1000G_30x)
C=0.1953 (978/5008, 1000G)
C=0.2923 (856/2928, KOREAN)
C=0.2838 (520/1832, Korea1K)
C=0.071 (71/998, GoNL)
C=0.183 (96/524, SGDP_PRJ)
C=0.111 (24/216, Qatari)
C=0.17 (2/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LAMP3 : 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	17330	C=0.10669	A=0.00000, G=0.89331
European	Sub	13466	C=0.07396	A=0.00000, G=0.92604
African	Sub	2398	C=0.2319	A=0.0000, G=0.7681
African Others	Sub	90	C=0.27	A=0.00, G=0.73
African American	Sub	2308	C=0.2305	A=0.0000, G=0.7695
Asian	Sub	112	C=0.286	A=0.000, G=0.714
East Asian	Sub	86	C=0.34	A=0.00, G=0.66
Other Asian	Sub	26	C=0.12	A=0.00, G=0.88
Latin American 1	Sub	146	C=0.116	A=0.000, G=0.884
Latin American 2	Sub	610	C=0.267	A=0.000, G=0.733
South Asian	Sub	98	C=0.14	A=0.00, G=0.86
Other	Sub	500	C=0.142	A=0.000, G=0.858

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=0.149469	G=0.850531
gnomAD - Genomes	Global	Study-wide	135236	C=0.133478	G=0.866522
gnomAD - Genomes	European	Sub	73626	C=0.07196	G=0.92804
gnomAD - Genomes	African	Sub	40054	C=0.21838	G=0.78162
gnomAD - Genomes	American	Sub	13126	C=0.20456	G=0.79544
gnomAD - Genomes	Ashkenazi Jewish	Sub	3290	C=0.0772	G=0.9228
gnomAD - Genomes	East Asian	Sub	3060	C=0.2641	G=0.7359
gnomAD - Genomes	Other	Sub	2080	C=0.1245	G=0.8755
14KJPN	JAPANESE	Study-wide	28254	C=0.26651	G=0.73349
Allele Frequency Aggregator	Total	Global	17330	C=0.10669	A=0.00000, G=0.89331
Allele Frequency Aggregator	European	Sub	13466	C=0.07396	A=0.00000, G=0.92604
Allele Frequency Aggregator	African	Sub	2398	C=0.2319	A=0.0000, G=0.7681
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.267	A=0.000, G=0.733
Allele Frequency Aggregator	Other	Sub	500	C=0.142	A=0.000, G=0.858
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.116	A=0.000, G=0.884
Allele Frequency Aggregator	Asian	Sub	112	C=0.286	A=0.000, G=0.714
Allele Frequency Aggregator	South Asian	Sub	98	C=0.14	A=0.00, G=0.86
8.3KJPN	JAPANESE	Study-wide	16760	C=0.26319	G=0.73681
1000Genomes_30x	Global	Study-wide	6404	C=0.1971	G=0.8029
1000Genomes_30x	African	Sub	1786	C=0.2268	G=0.7732
1000Genomes_30x	Europe	Sub	1266	C=0.0782	G=0.9218
1000Genomes_30x	South Asian	Sub	1202	C=0.1930	G=0.8070
1000Genomes_30x	East Asian	Sub	1170	C=0.2718	G=0.7282
1000Genomes_30x	American	Sub	980	C=0.212	G=0.788
1000Genomes	Global	Study-wide	5008	C=0.1953	G=0.8047
1000Genomes	African	Sub	1322	C=0.2201	G=0.7799
1000Genomes	East Asian	Sub	1008	C=0.2788	G=0.7212
1000Genomes	Europe	Sub	1006	C=0.0726	G=0.9274
1000Genomes	South Asian	Sub	978	C=0.187	G=0.813
1000Genomes	American	Sub	694	C=0.216	G=0.784
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.2923	A=0.0000, G=0.7077, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2838	G=0.7162
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.071	G=0.929
SGDP_PRJ	Global	Study-wide	524	C=0.183	G=0.817
Qatari	Global	Study-wide	216	C=0.111	G=0.889
Siberian	Global	Study-wide	12	C=0.17	G=0.83

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 3	NC_000003.12:g.183128137C>A
GRCh38.p14 chr 3	NC_000003.12:g.183128137C>G
GRCh38.p14 chr 3	NC_000003.12:g.183128137C>T
GRCh37.p13 chr 3	NC_000003.11:g.182845925C>A
GRCh37.p13 chr 3	NC_000003.11:g.182845925C>G
GRCh37.p13 chr 3	NC_000003.11:g.182845925C>T

Gene: LAMP3, lysosomal associated membrane protein 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LAMP3 transcript	NM_014398.4:c.1118-3923G>T	N/A	Intron Variant
LAMP3 transcript variant X1	XM_005247360.6:c.*4680=	N/A	3 Prime UTR Variant
LAMP3 transcript variant X3	XM_011512688.3:c.	N/A	Genic Downstream Transcript Variant
LAMP3 transcript variant X2	XM_047447967.1: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	C=	A	G	T
GRCh38.p14 chr 3	NC_000003.12:g.183128137=	NC_000003.12:g.183128137C>A	NC_000003.12:g.183128137C>G	NC_000003.12:g.183128137C>T
GRCh37.p13 chr 3	NC_000003.11:g.182845925=	NC_000003.11:g.182845925C>A	NC_000003.11:g.182845925C>G	NC_000003.11:g.182845925C>T
LAMP3 transcript variant X1	XM_005247360.6:c.*4680=	XM_005247360.6:c.*4680G>T	XM_005247360.6:c.*4680G>C	XM_005247360.6:c.*4680G>A
LAMP3 transcript	NM_014398.3:c.1118-3923=	NM_014398.3:c.1118-3923G>T	NM_014398.3:c.1118-3923G>C	NM_014398.3:c.1118-3923G>A
LAMP3 transcript	NM_014398.4:c.1118-3923=	NM_014398.4:c.1118-3923G>T	NM_014398.4:c.1118-3923G>C	NM_014398.4:c.1118-3923G>A
LAMP3 transcript variant X2	XM_005247361.1:c.1046-3923=	XM_005247361.1:c.1046-3923G>T	XM_005247361.1:c.1046-3923G>C	XM_005247361.1:c.1046-3923G>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#.

61 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss769898	Aug 11, 2000 (83)
2	BCM_SSAHASNP	ss10044446	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss17723975	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss19504534	Feb 27, 2004 (120)
5	SSAHASNP	ss21868261	Apr 05, 2004 (121)
6	HGSV	ss77580310	Dec 07, 2007 (129)
7	HGSV	ss78430456	Dec 07, 2007 (129)
8	HGSV	ss84102742	Dec 14, 2007 (130)
9	BCMHGSC_JDW	ss92395202	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss99154389	Feb 04, 2009 (130)
11	ENSEMBL	ss135409264	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss162887094	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss165172394	Jul 04, 2010 (132)
14	BUSHMAN	ss203618716	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss206192616	Jul 04, 2010 (132)
16	BL	ss253728445	May 09, 2011 (134)
17	GMI	ss277484354	May 04, 2012 (137)
18	GMI	ss284806183	Apr 25, 2013 (138)
19	PJP	ss292987959	May 09, 2011 (134)
20	1000GENOMES	ss331292192	May 09, 2011 (134)
21	TISHKOFF	ss557167109	Apr 25, 2013 (138)
22	EVA-GONL	ss979537979	Aug 21, 2014 (142)
23	1000GENOMES	ss1307586351	Aug 21, 2014 (142)
24	DDI	ss1429695790	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1800557991	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1922757523	Feb 12, 2016 (147)
27	GENOMED	ss1969607636	Jul 19, 2016 (147)
28	JJLAB	ss2021954721	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2150052454	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2625475831	Nov 08, 2017 (151)
31	GRF	ss2705475474	Nov 08, 2017 (151)
32	GNOMAD	ss2803240207	Nov 08, 2017 (151)
33	SWEGEN	ss2993767053	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3024745422	Nov 08, 2017 (151)
35	CSHL	ss3345428870	Nov 08, 2017 (151)
36	URBANLAB	ss3647601479	Oct 12, 2018 (152)
37	EVA	ss3761128243	Jul 13, 2019 (153)
38	PACBIO	ss3784556873	Jul 13, 2019 (153)
39	PACBIO	ss3790035110	Jul 13, 2019 (153)
40	PACBIO	ss3794909816	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3804265422	Jul 13, 2019 (153)
42	EVA	ss3828256688	Apr 25, 2020 (154)
43	EVA	ss3837560309	Apr 25, 2020 (154)
44	EVA	ss3842992793	Apr 25, 2020 (154)
45	SGDP_PRJ	ss3857725390	Apr 25, 2020 (154)
46	KRGDB	ss3903809493	Apr 25, 2020 (154)
47	KOGIC	ss3953092084	Apr 25, 2020 (154)
48	TOPMED	ss4596144113	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5163199471	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5257276421	Oct 13, 2022 (156)
51	EVA	ss5345556938	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5456296467	Oct 13, 2022 (156)
53	EVA	ss5507334235	Oct 13, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5537379062	Oct 13, 2022 (156)
55	SANFORD_IMAGENETICS	ss5633905117	Oct 13, 2022 (156)
56	TOMMO_GENOMICS	ss5696540354	Oct 13, 2022 (156)
57	YY_MCH	ss5804554407	Oct 13, 2022 (156)
58	EVA	ss5826961908	Oct 13, 2022 (156)
59	EVA	ss5872437372	Oct 13, 2022 (156)
60	EVA	ss5962287205	Oct 13, 2022 (156)
61	EVA	ss5980190318	Oct 13, 2022 (156)
62	1000Genomes	NC_000003.11 - 182845925	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000003.12 - 183128137	Oct 13, 2022 (156)
64	gnomAD - Genomes	NC_000003.12 - 183128137	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000003.11 - 182845925	Apr 25, 2020 (154)
66	KOREAN population from KRGDB	NC_000003.11 - 182845925	Apr 25, 2020 (154)
67	Korean Genome Project	NC_000003.12 - 183128137	Apr 25, 2020 (154)
68	Qatari	NC_000003.11 - 182845925	Apr 25, 2020 (154)
69	SGDP_PRJ	NC_000003.11 - 182845925	Apr 25, 2020 (154)
70	Siberian	NC_000003.11 - 182845925	Apr 25, 2020 (154)
71	8.3KJPN	NC_000003.11 - 182845925	Apr 26, 2021 (155)
72	14KJPN	NC_000003.12 - 183128137	Oct 13, 2022 (156)
73	TopMed	NC_000003.12 - 183128137	Apr 26, 2021 (155)
74	ALFA	NC_000003.12 - 183128137	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).

Associated ID	History Updated (Build)
rs57354119	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10986887, ss3903809493	NC_000003.11:182845924:C:A	NC_000003.12:183128136:C:A	(self)
11708928424	NC_000003.12:183128136:C:A	NC_000003.12:183128136:C:A	(self)
ss77580310, ss78430456, ss84102742	NC_000003.9:184328626:C:G	NC_000003.12:183128136:C:G	(self)
ss92395202, ss162887094, ss165172394, ss203618716, ss206192616, ss253728445, ss277484354, ss284806183, ss292987959	NC_000003.10:184328618:C:G	NC_000003.12:183128136:C:G	(self)
18905031, 4630270, 10986887, 4799453, 9742370, 2568808, 21168778, ss331292192, ss557167109, ss979537979, ss1307586351, ss1429695790, ss1800557991, ss1922757523, ss1969607636, ss2021954721, ss2150052454, ss2625475831, ss2705475474, ss2803240207, ss2993767053, ss3345428870, ss3761128243, ss3784556873, ss3790035110, ss3794909816, ss3828256688, ss3837560309, ss3857725390, ss3903809493, ss5163199471, ss5345556938, ss5507334235, ss5633905117, ss5826961908, ss5962287205, ss5980190318	NC_000003.11:182845924:C:G	NC_000003.12:183128136:C:G	(self)
24904997, 134307185, 9470085, 30377458, 433521668, 11708928424, ss3024745422, ss3647601479, ss3804265422, ss3842992793, ss3953092084, ss4596144113, ss5257276421, ss5456296467, ss5537379062, ss5696540354, ss5804554407, ss5872437372	NC_000003.12:183128136:C:G	NC_000003.12:183128136:C:G	(self)
ss17723975, ss19504534, ss21868261	NT_005612.14:89341082:C:G	NC_000003.12:183128136:C:G	(self)
ss769898, ss99154389, ss135409264	NT_005612.16:89341070:C:G	NC_000003.12:183128136:C:G	(self)
ss10044446	NT_005962.15:18058387:C:G	NC_000003.12:183128136:C:G	(self)
10986887, ss3903809493	NC_000003.11:182845924:C:T	NC_000003.12:183128136:C: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 rs598002

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

rs598002