Name: rs1001930
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.

rs1001930

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:209653448 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.264657 (70052/264690, TOPMED)
G=0.263978 (37005/140182, GnomAD)
G=0.23826 (7339/30802, ALFA) (+ 16 more)
G=0.40027 (11310/28256, 14KJPN)
G=0.39797 (6670/16760, 8.3KJPN)
G=0.3148 (2016/6404, 1000G_30x)
G=0.3139 (1572/5008, 1000G)
G=0.2446 (1096/4480, Estonian)
G=0.2122 (818/3854, ALSPAC)
G=0.2077 (770/3708, TWINSUK)
G=0.4857 (1423/2930, KOREAN)
G=0.4389 (804/1832, Korea1K)
G=0.214 (214/998, GoNL)
G=0.232 (139/600, NorthernSweden)
A=0.383 (102/266, SGDP_PRJ)
G=0.259 (56/216, Qatari)
G=0.231 (49/212, Vietnamese)
A=0.36 (15/42, Siberian)
G=0.28 (11/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LAMB3 : 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	30802	A=0.76174	G=0.23826
European	Sub	24672	A=0.77537	G=0.22463
African	Sub	3168	A=0.6736	G=0.3264
African Others	Sub	124	A=0.661	G=0.339
African American	Sub	3044	A=0.6741	G=0.3259
Asian	Sub	128	A=0.594	G=0.406
East Asian	Sub	100	A=0.52	G=0.48
Other Asian	Sub	28	A=0.86	G=0.14
Latin American 1	Sub	168	A=0.768	G=0.232
Latin American 2	Sub	700	A=0.763	G=0.237
South Asian	Sub	114	A=0.640	G=0.360
Other	Sub	1852	A=0.7489	G=0.2511

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	A=0.735343	G=0.264657
gnomAD - Genomes	Global	Study-wide	140182	A=0.736022	G=0.263978
gnomAD - Genomes	European	Sub	75918	A=0.77092	G=0.22908
gnomAD - Genomes	African	Sub	41998	A=0.67972	G=0.32028
gnomAD - Genomes	American	Sub	13662	A=0.75143	G=0.24857
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.7170	G=0.2830
gnomAD - Genomes	East Asian	Sub	3132	A=0.6012	G=0.3988
gnomAD - Genomes	Other	Sub	2150	A=0.7312	G=0.2688
Allele Frequency Aggregator	Total	Global	30802	A=0.76174	G=0.23826
Allele Frequency Aggregator	European	Sub	24672	A=0.77537	G=0.22463
Allele Frequency Aggregator	African	Sub	3168	A=0.6736	G=0.3264
Allele Frequency Aggregator	Other	Sub	1852	A=0.7489	G=0.2511
Allele Frequency Aggregator	Latin American 2	Sub	700	A=0.763	G=0.237
Allele Frequency Aggregator	Latin American 1	Sub	168	A=0.768	G=0.232
Allele Frequency Aggregator	Asian	Sub	128	A=0.594	G=0.406
Allele Frequency Aggregator	South Asian	Sub	114	A=0.640	G=0.360
14KJPN	JAPANESE	Study-wide	28256	A=0.59973	G=0.40027
8.3KJPN	JAPANESE	Study-wide	16760	A=0.60203	G=0.39797
1000Genomes_30x	Global	Study-wide	6404	A=0.6852	G=0.3148
1000Genomes_30x	African	Sub	1786	A=0.6557	G=0.3443
1000Genomes_30x	Europe	Sub	1266	A=0.7773	G=0.2227
1000Genomes_30x	South Asian	Sub	1202	A=0.6572	G=0.3428
1000Genomes_30x	East Asian	Sub	1170	A=0.6214	G=0.3786
1000Genomes_30x	American	Sub	980	A=0.731	G=0.269
1000Genomes	Global	Study-wide	5008	A=0.6861	G=0.3139
1000Genomes	African	Sub	1322	A=0.6536	G=0.3464
1000Genomes	East Asian	Sub	1008	A=0.6300	G=0.3700
1000Genomes	Europe	Sub	1006	A=0.7763	G=0.2237
1000Genomes	South Asian	Sub	978	A=0.665	G=0.335
1000Genomes	American	Sub	694	A=0.729	G=0.271
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7554	G=0.2446
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7878	G=0.2122
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7923	G=0.2077
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5143	C=0.0000, G=0.4857
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5611	G=0.4389
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.786	G=0.214
Northern Sweden	ACPOP	Study-wide	600	A=0.768	G=0.232
SGDP_PRJ	Global	Study-wide	266	A=0.383	G=0.617
Qatari	Global	Study-wide	216	A=0.741	G=0.259
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.769	G=0.231
Siberian	Global	Study-wide	42	A=0.36	G=0.64
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28

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.209653448A>C
GRCh38.p14 chr 1	NC_000001.11:g.209653448A>G
GRCh37.p13 chr 1	NC_000001.10:g.209826793A>C
GRCh37.p13 chr 1	NC_000001.10:g.209826793A>G
LAMB3 RefSeqGene	NG_007116.1:g.4028T>G
LAMB3 RefSeqGene	NG_007116.1:g.4028T>C

Gene: LAMB3, laminin subunit beta 3 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LAMB3 transcript variant 1	NM_000228.3:c.	N/A	Upstream Transcript Variant
LAMB3 transcript variant 3	NM_001127641.1:c.	N/A	Upstream Transcript Variant
LAMB3 transcript variant 2	NM_001017402.2:c.	N/A	N/A
LAMB3 transcript variant X1	XM_005273124.5:c.	N/A	Upstream Transcript Variant
LAMB3 transcript variant X2	XM_017001272.3:c.	N/A	Upstream Transcript Variant
LAMB3 transcript variant X3	XM_047420351.1:c.	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	A=	C	G
GRCh38.p14 chr 1	NC_000001.11:g.209653448=	NC_000001.11:g.209653448A>C	NC_000001.11:g.209653448A>G
GRCh37.p13 chr 1	NC_000001.10:g.209826793=	NC_000001.10:g.209826793A>C	NC_000001.10:g.209826793A>G
LAMB3 RefSeqGene	NG_007116.1:g.4028=	NG_007116.1:g.4028T>G	NG_007116.1:g.4028T>C

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#.

82 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1462378	Oct 05, 2000 (86)
2	YUSUKE	ss2987816	Jun 15, 2001 (96)
3	HGBASE	ss3188562	Aug 15, 2001 (98)
4	WI_SSAHASNP	ss6692433	Feb 20, 2003 (111)
5	BCM_SSAHASNP	ss9858083	Jul 11, 2003 (116)
6	WI_SSAHASNP	ss11133617	Jul 11, 2003 (116)
7	SC_JCM	ss11202701	Jul 11, 2003 (116)
8	SC_JCM	ss13504792	Dec 05, 2003 (119)
9	BCM_SSAHASNP	ss13540695	Dec 05, 2003 (119)
10	WI_SSAHASNP	ss13621348	Dec 05, 2003 (119)
11	SSAHASNP	ss35236237	May 24, 2005 (125)
12	ABI	ss41072327	Mar 15, 2006 (126)
13	HGSV	ss84650416	Dec 16, 2007 (130)
14	1000GENOMES	ss108909274	Jan 23, 2009 (130)
15	1000GENOMES	ss111704317	Jan 25, 2009 (130)
16	COMPLETE_GENOMICS	ss165037696	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss167470088	Jul 04, 2010 (132)
18	BUSHMAN	ss199551049	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss205339900	Jul 04, 2010 (132)
20	1000GENOMES	ss218855718	Jul 14, 2010 (132)
21	1000GENOMES	ss230881356	Jul 14, 2010 (132)
22	1000GENOMES	ss238498141	Jul 15, 2010 (132)
23	BL	ss253791221	May 09, 2011 (134)
24	GMI	ss276198150	May 04, 2012 (137)
25	GMI	ss284219735	Apr 25, 2013 (138)
26	PJP	ss290723951	May 09, 2011 (134)
27	ILLUMINA	ss482213770	May 04, 2012 (137)
28	ILLUMINA	ss484219329	May 04, 2012 (137)
29	ILLUMINA	ss536406035	Sep 08, 2015 (146)
30	TISHKOFF	ss555108877	Apr 25, 2013 (138)
31	SSMP	ss648665703	Apr 25, 2013 (138)
32	ILLUMINA	ss779528829	Sep 08, 2015 (146)
33	ILLUMINA	ss782555682	Sep 08, 2015 (146)
34	ILLUMINA	ss834999373	Sep 08, 2015 (146)
35	EVA-GONL	ss976090408	Aug 21, 2014 (142)
36	JMKIDD_LAB	ss1068561774	Aug 21, 2014 (142)
37	1000GENOMES	ss1294451338	Aug 21, 2014 (142)
38	DDI	ss1426096300	Apr 01, 2015 (144)
39	EVA_GENOME_DK	ss1574643622	Apr 01, 2015 (144)
40	EVA_DECODE	ss1585485944	Apr 01, 2015 (144)
41	EVA_UK10K_ALSPAC	ss1602032876	Apr 01, 2015 (144)
42	EVA_UK10K_TWINSUK	ss1645026909	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1795661223	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1919316477	Feb 12, 2016 (147)
45	GENOMED	ss1966960482	Jul 19, 2016 (147)
46	JJLAB	ss2020179869	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2148209644	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2169675798	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2624598880	Nov 08, 2017 (151)
50	ILLUMINA	ss2632623069	Nov 08, 2017 (151)
51	GRF	ss2698202304	Nov 08, 2017 (151)
52	GNOMAD	ss2765655863	Nov 08, 2017 (151)
53	SWEGEN	ss2988368233	Nov 08, 2017 (151)
54	BIOINF_KMB_FNS_UNIBA	ss3023849636	Nov 08, 2017 (151)
55	CSHL	ss3343888166	Nov 08, 2017 (151)
56	ILLUMINA	ss3626297137	Oct 11, 2018 (152)
57	ILLUMINA	ss3630653231	Oct 11, 2018 (152)
58	EGCUT_WGS	ss3656326499	Jul 12, 2019 (153)
59	EVA_DECODE	ss3688532220	Jul 12, 2019 (153)
60	ACPOP	ss3727818016	Jul 12, 2019 (153)
61	EVA	ss3747273706	Jul 12, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3800279321	Jul 12, 2019 (153)
63	EVA	ss3826617316	Apr 25, 2020 (154)
64	EVA	ss3836708905	Apr 25, 2020 (154)
65	EVA	ss3842120408	Apr 25, 2020 (154)
66	SGDP_PRJ	ss3850794986	Apr 25, 2020 (154)
67	KRGDB	ss3896098614	Apr 25, 2020 (154)
68	KOGIC	ss3946395577	Apr 25, 2020 (154)
69	TOPMED	ss4481829630	Apr 27, 2021 (155)
70	TOMMO_GENOMICS	ss5148209589	Apr 27, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5245623613	Oct 12, 2022 (156)
72	EVA	ss5314678658	Oct 12, 2022 (156)
73	EVA	ss5324476926	Oct 12, 2022 (156)
74	HUGCELL_USP	ss5446077744	Oct 12, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5519633333	Oct 12, 2022 (156)
76	SANFORD_IMAGENETICS	ss5627349466	Oct 12, 2022 (156)
77	TOMMO_GENOMICS	ss5675906363	Oct 12, 2022 (156)
78	YY_MCH	ss5801594475	Oct 12, 2022 (156)
79	EVA	ss5833191881	Oct 12, 2022 (156)
80	EVA	ss5849262861	Oct 12, 2022 (156)
81	EVA	ss5911774006	Oct 12, 2022 (156)
82	EVA	ss5939181936	Oct 12, 2022 (156)
83	1000Genomes	NC_000001.10 - 209826793	Oct 11, 2018 (152)
84	1000Genomes_30x	NC_000001.11 - 209653448	Oct 12, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 209826793	Oct 11, 2018 (152)
86	Genetic variation in the Estonian population	NC_000001.10 - 209826793	Oct 11, 2018 (152)
87	The Danish reference pan genome	NC_000001.10 - 209826793	Apr 25, 2020 (154)
88	gnomAD - Genomes	NC_000001.11 - 209653448	Apr 27, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000001.10 - 209826793	Apr 25, 2020 (154)
90	KOREAN population from KRGDB	NC_000001.10 - 209826793	Apr 25, 2020 (154)
91	Korean Genome Project	NC_000001.11 - 209653448	Apr 25, 2020 (154)
92	Northern Sweden	NC_000001.10 - 209826793	Jul 12, 2019 (153)
93	Qatari	NC_000001.10 - 209826793	Apr 25, 2020 (154)
94	SGDP_PRJ	NC_000001.10 - 209826793	Apr 25, 2020 (154)
95	Siberian	NC_000001.10 - 209826793	Apr 25, 2020 (154)
96	8.3KJPN	NC_000001.10 - 209826793	Apr 27, 2021 (155)
97	14KJPN	NC_000001.11 - 209653448	Oct 12, 2022 (156)
98	TopMed	NC_000001.11 - 209653448	Apr 27, 2021 (155)
99	UK 10K study - Twins	NC_000001.10 - 209826793	Oct 11, 2018 (152)
100	A Vietnamese Genetic Variation Database	NC_000001.10 - 209826793	Jul 12, 2019 (153)
101	ALFA	NC_000001.11 - 209653448	Apr 27, 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)
rs61480594	May 26, 2008 (130)
rs117649518	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
3276008, ss3896098614	NC_000001.10:209826792:A:C	NC_000001.11:209653447:A:C	(self)
ss2987816, ss3188562	NT_167186.1:3344571:A:C	NC_000001.11:209653447:A:C	(self)
ss35236237, ss84650416	NC_000001.8:206215187:A:G	NC_000001.11:209653447:A:G	(self)
ss108909274, ss111704317, ss165037696, ss167470088, ss199551049, ss205339900, ss253791221, ss276198150, ss284219735, ss290723951, ss482213770, ss1585485944	NC_000001.9:207893415:A:G	NC_000001.11:209653447:A:G	(self)
5298457, 2921099, 2064747, 1863649, 1274964, 3276008, 1102881, 1358407, 2811966, 725998, 6178896, 2921099, 630716, ss218855718, ss230881356, ss238498141, ss484219329, ss536406035, ss555108877, ss648665703, ss779528829, ss782555682, ss834999373, ss976090408, ss1068561774, ss1294451338, ss1426096300, ss1574643622, ss1602032876, ss1645026909, ss1795661223, ss1919316477, ss1966960482, ss2020179869, ss2148209644, ss2624598880, ss2632623069, ss2698202304, ss2765655863, ss2988368233, ss3343888166, ss3626297137, ss3630653231, ss3656326499, ss3727818016, ss3747273706, ss3826617316, ss3836708905, ss3850794986, ss3896098614, ss5148209589, ss5314678658, ss5324476926, ss5627349466, ss5833191881, ss5939181936	NC_000001.10:209826792:A:G	NC_000001.11:209653447:A:G	(self)
7159268, 38147033, 2773578, 9743467, 45435965, 10626847701, ss2169675798, ss3023849636, ss3688532220, ss3800279321, ss3842120408, ss3946395577, ss4481829630, ss5245623613, ss5446077744, ss5519633333, ss5675906363, ss5801594475, ss5849262861, ss5911774006	NC_000001.11:209653447:A:G	NC_000001.11:209653447:A:G	(self)
ss9858083, ss11133617, ss11202701	NT_021877.15:3285589:A:G	NC_000001.11:209653447:A:G	(self)
ss13504792, ss13540695, ss13621348	NT_021877.16:3285589:A:G	NC_000001.11:209653447:A:G	(self)
ss1462378, ss6692433, ss41072327	NT_167186.1:3344571:A:G	NC_000001.11:209653447:A:G	(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 rs1001930

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

rs1001930