Name: rs9293370
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.

rs9293370

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:84362671 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.261238 (69147/264690, TOPMED)
A=0.270979 (37904/139878, GnomAD)
A=0.06147 (1737/28258, 14KJPN) (+ 18 more)
A=0.32282 (6098/18890, ALFA)
A=0.06062 (1016/16760, 8.3KJPN)
A=0.1869 (1197/6404, 1000G_30x)
A=0.1895 (949/5008, 1000G)
A=0.3674 (1646/4480, Estonian)
A=0.3703 (1427/3854, ALSPAC)
A=0.3773 (1399/3708, TWINSUK)
A=0.0818 (239/2922, KOREAN)
A=0.0846 (155/1832, Korea1K)
A=0.370 (369/998, GoNL)
A=0.397 (238/600, NorthernSweden)
A=0.143 (47/328, HapMap)
A=0.486 (105/216, Qatari)
A=0.060 (13/216, Vietnamese)
T=0.410 (87/212, SGDP_PRJ)
A=0.22 (14/64, Ancient Sardinia)
A=0.30 (12/40, GENOME_DK)
T=0.27 (8/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EDIL3 : 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	18890	T=0.67718	A=0.32282
European	Sub	14286	T=0.62054	A=0.37946
African	Sub	2946	T=0.9192	A=0.0808
African Others	Sub	114	T=1.000	A=0.000
African American	Sub	2832	T=0.9160	A=0.0840
Asian	Sub	112	T=0.973	A=0.027
East Asian	Sub	86	T=0.97	A=0.03
Other Asian	Sub	26	T=1.00	A=0.00
Latin American 1	Sub	146	T=0.719	A=0.281
Latin American 2	Sub	610	T=0.703	A=0.297
South Asian	Sub	98	T=0.73	A=0.27
Other	Sub	692	T=0.728	A=0.272

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=0.738762	A=0.261238
gnomAD - Genomes	Global	Study-wide	139878	T=0.729021	A=0.270979
gnomAD - Genomes	European	Sub	75734	T=0.62849	A=0.37151
gnomAD - Genomes	African	Sub	41942	T=0.91421	A=0.08579
gnomAD - Genomes	American	Sub	13618	T=0.69746	A=0.30254
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.6346	A=0.3654
gnomAD - Genomes	East Asian	Sub	3116	T=0.9272	A=0.0728
gnomAD - Genomes	Other	Sub	2148	T=0.7160	A=0.2840
14KJPN	JAPANESE	Study-wide	28258	T=0.93853	A=0.06147
Allele Frequency Aggregator	Total	Global	18890	T=0.67718	A=0.32282
Allele Frequency Aggregator	European	Sub	14286	T=0.62054	A=0.37946
Allele Frequency Aggregator	African	Sub	2946	T=0.9192	A=0.0808
Allele Frequency Aggregator	Other	Sub	692	T=0.728	A=0.272
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.703	A=0.297
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.719	A=0.281
Allele Frequency Aggregator	Asian	Sub	112	T=0.973	A=0.027
Allele Frequency Aggregator	South Asian	Sub	98	T=0.73	A=0.27
8.3KJPN	JAPANESE	Study-wide	16760	T=0.93938	A=0.06062
1000Genomes_30x	Global	Study-wide	6404	T=0.8131	A=0.1869
1000Genomes_30x	African	Sub	1786	T=0.9591	A=0.0409
1000Genomes_30x	Europe	Sub	1266	T=0.6461	A=0.3539
1000Genomes_30x	South Asian	Sub	1202	T=0.7321	A=0.2679
1000Genomes_30x	East Asian	Sub	1170	T=0.9368	A=0.0632
1000Genomes_30x	American	Sub	980	T=0.714	A=0.286
1000Genomes	Global	Study-wide	5008	T=0.8105	A=0.1895
1000Genomes	African	Sub	1322	T=0.9569	A=0.0431
1000Genomes	East Asian	Sub	1008	T=0.9335	A=0.0665
1000Genomes	Europe	Sub	1006	T=0.6441	A=0.3559
1000Genomes	South Asian	Sub	978	T=0.726	A=0.274
1000Genomes	American	Sub	694	T=0.713	A=0.287
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6326	A=0.3674
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6297	A=0.3703
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6227	A=0.3773
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9182	A=0.0818
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9154	A=0.0846
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.630	A=0.370
Northern Sweden	ACPOP	Study-wide	600	T=0.603	A=0.397
HapMap	Global	Study-wide	328	T=0.857	A=0.143
HapMap	African	Sub	120	T=0.992	A=0.008
HapMap	American	Sub	120	T=0.667	A=0.333
HapMap	Asian	Sub	88	T=0.93	A=0.07
Qatari	Global	Study-wide	216	T=0.514	A=0.486
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.940	A=0.060
SGDP_PRJ	Global	Study-wide	212	T=0.410	A=0.590
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	64	T=0.78	A=0.22
The Danish reference pan genome	Danish	Study-wide	40	T=0.70	A=0.30
Siberian	Global	Study-wide	30	T=0.27	A=0.73

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 5	NC_000005.10:g.84362671T>A
GRCh37.p13 chr 5	NC_000005.9:g.83658489T>A

Gene: EDIL3, EGF like repeats and discoidin domains 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EDIL3 transcript variant 2	NM_001278642.1:c.67+21637… NM_001278642.1:c.67+21637A>T	N/A	Intron Variant
EDIL3 transcript variant 1	NM_005711.5:c.67+21637A>T	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.

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	T=	A
GRCh38.p14 chr 5	NC_000005.10:g.84362671=	NC_000005.10:g.84362671T>A
GRCh37.p13 chr 5	NC_000005.9:g.83658489=	NC_000005.9:g.83658489T>A
EDIL3 transcript variant 2	NM_001278642.1:c.67+21637=	NM_001278642.1:c.67+21637A>T
EDIL3 transcript variant 1	NM_005711.4:c.67+21637=	NM_005711.4:c.67+21637A>T
EDIL3 transcript variant 1	NM_005711.5:c.67+21637=	NM_005711.5:c.67+21637A>T

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#.

59 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13908759	Dec 05, 2003 (119)
2	PERLEGEN	ss14913984	Dec 05, 2003 (119)
3	PERLEGEN	ss24621306	Sep 20, 2004 (123)
4	ABI	ss42509765	Mar 13, 2006 (126)
5	AFFY	ss65961671	Dec 01, 2006 (127)
6	HGSV	ss82717821	Dec 14, 2007 (130)
7	BCMHGSC_JDW	ss93157538	Mar 24, 2008 (129)
8	1000GENOMES	ss109179912	Jan 23, 2009 (130)
9	ENSEMBL	ss143253255	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss166761225	Jul 04, 2010 (132)
11	1000GENOMES	ss233018856	Jul 14, 2010 (132)
12	1000GENOMES	ss240175401	Jul 15, 2010 (132)
13	BL	ss253588136	May 09, 2011 (134)
14	GMI	ss278363087	May 04, 2012 (137)
15	TISHKOFF	ss558512686	Apr 25, 2013 (138)
16	SSMP	ss652386955	Apr 25, 2013 (138)
17	EVA-GONL	ss981765791	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1072777961	Aug 21, 2014 (142)
19	1000GENOMES	ss1315853764	Aug 21, 2014 (142)
20	DDI	ss1430403175	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1581214567	Apr 01, 2015 (144)
22	EVA_DECODE	ss1591283929	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1613288695	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1656282728	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1925020372	Feb 12, 2016 (147)
26	GENOMED	ss1970133099	Jul 19, 2016 (147)
27	JJLAB	ss2023116701	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2151273243	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2275273021	Dec 20, 2016 (150)
30	GRF	ss2706825924	Nov 08, 2017 (151)
31	GNOMAD	ss2826830228	Nov 08, 2017 (151)
32	SWEGEN	ss2997247723	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3025343615	Nov 08, 2017 (151)
34	CSHL	ss3346474415	Nov 08, 2017 (151)
35	EGCUT_WGS	ss3665128555	Jul 13, 2019 (153)
36	EVA_DECODE	ss3715052002	Jul 13, 2019 (153)
37	ACPOP	ss3732521570	Jul 13, 2019 (153)
38	EVA	ss3763658408	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3806825374	Jul 13, 2019 (153)
40	EVA	ss3829339109	Apr 26, 2020 (154)
41	EVA	ss3838143236	Apr 26, 2020 (154)
42	EVA	ss3843584425	Apr 26, 2020 (154)
43	SGDP_PRJ	ss3862263810	Apr 26, 2020 (154)
44	KRGDB	ss3908845901	Apr 26, 2020 (154)
45	KOGIC	ss3957041275	Apr 26, 2020 (154)
46	EVA	ss3985152497	Apr 26, 2021 (155)
47	TOPMED	ss4666602375	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5172625516	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5264649023	Oct 13, 2022 (156)
50	EVA	ss5358789403	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5462752772	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5548643703	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5638190659	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5709272619	Oct 13, 2022 (156)
55	YY_MCH	ss5806485372	Oct 13, 2022 (156)
56	EVA	ss5835186570	Oct 13, 2022 (156)
57	EVA	ss5854891225	Oct 13, 2022 (156)
58	EVA	ss5894947531	Oct 13, 2022 (156)
59	EVA	ss5966626304	Oct 13, 2022 (156)
60	1000Genomes	NC_000005.9 - 83658489	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000005.10 - 84362671	Oct 13, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 83658489	Oct 12, 2018 (152)
63	Genetic variation in the Estonian population	NC_000005.9 - 83658489	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000005.9 - 83658489	Apr 26, 2020 (154)
65	gnomAD - Genomes	NC_000005.10 - 84362671	Apr 26, 2021 (155)
66	Genome of the Netherlands Release 5	NC_000005.9 - 83658489	Apr 26, 2020 (154)
67	HapMap	NC_000005.10 - 84362671	Apr 26, 2020 (154)
68	KOREAN population from KRGDB	NC_000005.9 - 83658489	Apr 26, 2020 (154)
69	Korean Genome Project	NC_000005.10 - 84362671	Apr 26, 2020 (154)
70	Northern Sweden	NC_000005.9 - 83658489	Jul 13, 2019 (153)
71	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000005.9 - 83658489	Apr 26, 2021 (155)
72	Qatari	NC_000005.9 - 83658489	Apr 26, 2020 (154)
73	SGDP_PRJ	NC_000005.9 - 83658489	Apr 26, 2020 (154)
74	Siberian	NC_000005.9 - 83658489	Apr 26, 2020 (154)
75	8.3KJPN	NC_000005.9 - 83658489	Apr 26, 2021 (155)
76	14KJPN	NC_000005.10 - 84362671	Oct 13, 2022 (156)
77	TopMed	NC_000005.10 - 84362671	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000005.9 - 83658489	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000005.9 - 83658489	Jul 13, 2019 (153)
80	ALFA	NC_000005.10 - 84362671	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)
rs17284985	Oct 08, 2004 (123)
rs57137070	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82717821, ss93157538, ss109179912, ss166761225, ss253588136, ss278363087, ss1591283929	NC_000005.8:83694244:T:A	NC_000005.10:84362670:T:A	(self)
27482328, 15280957, 10866803, 7379506, 6793466, 16023295, 5806435, 378424, 7062302, 14280790, 3789597, 30594823, 15280957, 3391851, ss233018856, ss240175401, ss558512686, ss652386955, ss981765791, ss1072777961, ss1315853764, ss1430403175, ss1581214567, ss1613288695, ss1656282728, ss1925020372, ss1970133099, ss2023116701, ss2151273243, ss2706825924, ss2826830228, ss2997247723, ss3346474415, ss3665128555, ss3732521570, ss3763658408, ss3829339109, ss3838143236, ss3862263810, ss3908845901, ss3985152497, ss5172625516, ss5358789403, ss5638190659, ss5835186570, ss5966626304	NC_000005.9:83658488:T:A	NC_000005.10:84362670:T:A	(self)
36169638, 194280951, 2903971, 13419276, 43109723, 503979932, 14430036982, ss2275273021, ss3025343615, ss3715052002, ss3806825374, ss3843584425, ss3957041275, ss4666602375, ss5264649023, ss5462752772, ss5548643703, ss5709272619, ss5806485372, ss5854891225, ss5894947531	NC_000005.10:84362670:T:A	NC_000005.10:84362670:T:A	(self)
ss13908759	NT_006713.13:13050620:T:A	NC_000005.10:84362670:T:A	(self)
ss14913984, ss24621306, ss42509765, ss65961671, ss143253255	NT_006713.15:34252847:T:A	NC_000005.10:84362670:T:A	(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 rs9293370

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

rs9293370