Name: rs48407
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.

rs48407

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:50845487 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.262840 (69571/264690, TOPMED)
G=0.257080 (36004/140050, GnomAD)
G=0.21549 (17889/83014, ALFA) (+ 19 more)
G=0.37299 (10540/28258, 14KJPN)
G=0.37566 (6296/16760, 8.3KJPN)
G=0.2662 (1705/6404, 1000G_30x)
G=0.2628 (1316/5008, 1000G)
G=0.2092 (937/4480, Estonian)
G=0.1892 (729/3854, ALSPAC)
G=0.2047 (759/3708, TWINSUK)
G=0.3816 (1118/2930, KOREAN)
G=0.2469 (514/2082, HGDP_Stanford)
G=0.2769 (519/1874, HapMap)
G=0.3690 (676/1832, Korea1K)
G=0.197 (197/998, GoNL)
G=0.192 (115/600, NorthernSweden)
A=0.433 (104/240, SGDP_PRJ)
G=0.208 (45/216, Qatari)
G=0.252 (54/214, Vietnamese)
G=0.25 (22/88, Ancient Sardinia)
G=0.17 (7/40, GENOME_DK)
A=0.44 (16/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DLEU7-AS1 : Intron Variant
DLEU7 : 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	83014	A=0.78451	G=0.21549
European	Sub	69178	A=0.78957	G=0.21043
African	Sub	4724	A=0.6636	G=0.3364
African Others	Sub	180	A=0.600	G=0.400
African American	Sub	4544	A=0.6662	G=0.3338
Asian	Sub	202	A=0.698	G=0.302
East Asian	Sub	160	A=0.706	G=0.294
Other Asian	Sub	42	A=0.67	G=0.33
Latin American 1	Sub	268	A=0.709	G=0.291
Latin American 2	Sub	1314	A=0.7725	G=0.2275
South Asian	Sub	4966	A=0.8562	G=0.1438
Other	Sub	2362	A=0.7498	G=0.2502

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=0.737160	G=0.262840
gnomAD - Genomes	Global	Study-wide	140050	A=0.742920	G=0.257080
gnomAD - Genomes	European	Sub	75870	A=0.78823	G=0.21177
gnomAD - Genomes	African	Sub	41956	A=0.65712	G=0.34288
gnomAD - Genomes	American	Sub	13636	A=0.77860	G=0.22140
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.7259	G=0.2741
gnomAD - Genomes	East Asian	Sub	3128	A=0.6787	G=0.3213
gnomAD - Genomes	Other	Sub	2140	A=0.7117	G=0.2883
Allele Frequency Aggregator	Total	Global	83014	A=0.78451	G=0.21549
Allele Frequency Aggregator	European	Sub	69178	A=0.78957	G=0.21043
Allele Frequency Aggregator	South Asian	Sub	4966	A=0.8562	G=0.1438
Allele Frequency Aggregator	African	Sub	4724	A=0.6636	G=0.3364
Allele Frequency Aggregator	Other	Sub	2362	A=0.7498	G=0.2502
Allele Frequency Aggregator	Latin American 2	Sub	1314	A=0.7725	G=0.2275
Allele Frequency Aggregator	Latin American 1	Sub	268	A=0.709	G=0.291
Allele Frequency Aggregator	Asian	Sub	202	A=0.698	G=0.302
14KJPN	JAPANESE	Study-wide	28258	A=0.62701	G=0.37299
8.3KJPN	JAPANESE	Study-wide	16760	A=0.62434	G=0.37566
1000Genomes_30x	Global	Study-wide	6404	A=0.7338	G=0.2662
1000Genomes_30x	African	Sub	1786	A=0.6299	G=0.3701
1000Genomes_30x	Europe	Sub	1266	A=0.8009	G=0.1991
1000Genomes_30x	South Asian	Sub	1202	A=0.8478	G=0.1522
1000Genomes_30x	East Asian	Sub	1170	A=0.6778	G=0.3222
1000Genomes_30x	American	Sub	980	A=0.763	G=0.237
1000Genomes	Global	Study-wide	5008	A=0.7372	G=0.2628
1000Genomes	African	Sub	1322	A=0.6309	G=0.3691
1000Genomes	East Asian	Sub	1008	A=0.6806	G=0.3194
1000Genomes	Europe	Sub	1006	A=0.8002	G=0.1998
1000Genomes	South Asian	Sub	978	A=0.847	G=0.153
1000Genomes	American	Sub	694	A=0.777	G=0.223
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7908	G=0.2092
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8108	G=0.1892
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7953	G=0.2047
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6184	G=0.3816
HGDP-CEPH-db Supplement 1	Global	Study-wide	2082	A=0.7531	G=0.2469
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	A=0.702	G=0.298
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	A=0.771	G=0.229
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	A=0.751	G=0.249
HGDP-CEPH-db Supplement 1	Europe	Sub	320	A=0.822	G=0.178
HGDP-CEPH-db Supplement 1	Africa	Sub	240	A=0.679	G=0.321
HGDP-CEPH-db Supplement 1	America	Sub	216	A=0.764	G=0.236
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	A=0.90	G=0.10
HapMap	Global	Study-wide	1874	A=0.7231	G=0.2769
HapMap	American	Sub	766	A=0.756	G=0.244
HapMap	African	Sub	682	A=0.689	G=0.311
HapMap	Asian	Sub	250	A=0.652	G=0.348
HapMap	Europe	Sub	176	A=0.812	G=0.188
Korean Genome Project	KOREAN	Study-wide	1832	A=0.6310	G=0.3690
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.803	G=0.197
Northern Sweden	ACPOP	Study-wide	600	A=0.808	G=0.192
SGDP_PRJ	Global	Study-wide	240	A=0.433	G=0.567
Qatari	Global	Study-wide	216	A=0.792	G=0.208
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.748	G=0.252
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	88	A=0.75	G=0.25
The Danish reference pan genome	Danish	Study-wide	40	A=0.82	G=0.17
Siberian	Global	Study-wide	36	A=0.44	G=0.56

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 13	NC_000013.11:g.50845487A>G
GRCh37.p13 chr 13	NC_000013.10:g.51419623A>G

Gene: DLEU7, deleted in lymphocytic leukemia 7 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
DLEU7 transcript variant 1	NM_001306135.2:c.	N/A	Upstream Transcript Variant
DLEU7 transcript variant 2	NM_198989.3:c.	N/A	Upstream Transcript Variant

Gene: DLEU7-AS1, DLEU7 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DLEU7-AS1 transcript	NR_046551.1:n.	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	A=	G
GRCh38.p14 chr 13	NC_000013.11:g.50845487=	NC_000013.11:g.50845487A>G
GRCh37.p13 chr 13	NC_000013.10:g.51419623=	NC_000013.10:g.51419623A>G

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#.

100 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss54492	Oct 05, 2000 (92)
2	SC_JCM	ss685522	Aug 11, 2000 (83)
3	KWOK	ss935628	Oct 05, 2000 (87)
4	KWOK	ss1861189	Oct 18, 2000 (87)
5	TSC-CSHL	ss5567690	Oct 08, 2002 (108)
6	SC_SNP	ss13286102	Dec 05, 2003 (119)
7	ABI	ss43542076	Mar 13, 2006 (126)
8	ILLUMINA	ss66588557	Nov 30, 2006 (127)
9	ILLUMINA	ss67385856	Nov 30, 2006 (127)
10	ILLUMINA	ss67761835	Nov 30, 2006 (127)
11	ILLUMINA	ss70829583	May 25, 2008 (130)
12	ILLUMINA	ss71412080	May 17, 2007 (127)
13	ILLUMINA	ss74929214	Dec 06, 2007 (129)
14	ILLUMINA	ss79198342	Dec 15, 2007 (130)
15	KRIBB_YJKIM	ss83361421	Dec 15, 2007 (130)
16	1000GENOMES	ss114702952	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss118723964	Feb 14, 2009 (130)
18	ILLUMINA	ss122406133	Dec 01, 2009 (131)
19	ILLUMINA	ss154322153	Dec 01, 2009 (131)
20	GMI	ss154805523	Dec 01, 2009 (131)
21	ILLUMINA	ss159498764	Dec 01, 2009 (131)
22	COMPLETE_GENOMICS	ss168110518	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss169577709	Jul 04, 2010 (132)
24	ILLUMINA	ss171942700	Jul 04, 2010 (132)
25	ILLUMINA	ss173839499	Jul 04, 2010 (132)
26	1000GENOMES	ss226188040	Jul 14, 2010 (132)
27	1000GENOMES	ss236254442	Jul 15, 2010 (132)
28	1000GENOMES	ss242750243	Jul 15, 2010 (132)
29	GMI	ss281715940	May 04, 2012 (137)
30	GMI	ss286705398	Apr 25, 2013 (138)
31	ILLUMINA	ss410936724	Sep 17, 2011 (135)
32	ILLUMINA	ss483202459	May 04, 2012 (137)
33	ILLUMINA	ss483255558	May 04, 2012 (137)
34	ILLUMINA	ss535473436	Sep 08, 2015 (146)
35	TISHKOFF	ss563670870	Apr 25, 2013 (138)
36	SSMP	ss659275755	Apr 25, 2013 (138)
37	ILLUMINA	ss780209210	Sep 08, 2015 (146)
38	ILLUMINA	ss782071266	Sep 08, 2015 (146)
39	ILLUMINA	ss825528860	Apr 01, 2015 (144)
40	ILLUMINA	ss833010130	Jul 13, 2019 (153)
41	ILLUMINA	ss835693995	Sep 08, 2015 (146)
42	EVA-GONL	ss990396108	Aug 21, 2014 (142)
43	JMKIDD_LAB	ss1079088699	Aug 21, 2014 (142)
44	1000GENOMES	ss1348234911	Aug 21, 2014 (142)
45	DDI	ss1427189616	Apr 01, 2015 (144)
46	EVA_GENOME_DK	ss1576790622	Apr 01, 2015 (144)
47	EVA_UK10K_ALSPAC	ss1630291358	Apr 01, 2015 (144)
48	EVA_UK10K_TWINSUK	ss1673285391	Apr 01, 2015 (144)
49	EVA_DECODE	ss1684920166	Apr 01, 2015 (144)
50	EVA_SVP	ss1713391830	Apr 01, 2015 (144)
51	HAMMER_LAB	ss1807612894	Sep 08, 2015 (146)
52	WEILL_CORNELL_DGM	ss1933763798	Feb 12, 2016 (147)
53	GENOMED	ss1967784083	Jul 19, 2016 (147)
54	JJLAB	ss2027642998	Sep 14, 2016 (149)
55	USC_VALOUEV	ss2156008754	Dec 20, 2016 (150)
56	HUMAN_LONGEVITY	ss2196358885	Dec 20, 2016 (150)
57	SYSTEMSBIOZJU	ss2628311342	Nov 08, 2017 (151)
58	ILLUMINA	ss2633065114	Nov 08, 2017 (151)
59	GRF	ss2700388221	Nov 08, 2017 (151)
60	GNOMAD	ss2919686996	Nov 08, 2017 (151)
61	SWEGEN	ss3011026389	Nov 08, 2017 (151)
62	BIOINF_KMB_FNS_UNIBA	ss3027637853	Nov 08, 2017 (151)
63	CSHL	ss3350457746	Nov 08, 2017 (151)
64	ILLUMINA	ss3627067124	Oct 12, 2018 (152)
65	ILLUMINA	ss3631068387	Oct 12, 2018 (152)
66	ILLUMINA	ss3638011901	Oct 12, 2018 (152)
67	ILLUMINA	ss3639018923	Oct 12, 2018 (152)
68	ILLUMINA	ss3639512882	Oct 12, 2018 (152)
69	ILLUMINA	ss3641839068	Oct 12, 2018 (152)
70	ILLUMINA	ss3643001578	Oct 12, 2018 (152)
71	URBANLAB	ss3650033970	Oct 12, 2018 (152)
72	EGCUT_WGS	ss3678292101	Jul 13, 2019 (153)
73	EVA_DECODE	ss3695298720	Jul 13, 2019 (153)
74	ACPOP	ss3739750356	Jul 13, 2019 (153)
75	EVA	ss3751468481	Jul 13, 2019 (153)
76	KHV_HUMAN_GENOMES	ss3816798957	Jul 13, 2019 (153)
77	EVA	ss3833548794	Apr 27, 2020 (154)
78	EVA	ss3840355904	Apr 27, 2020 (154)
79	EVA	ss3845841745	Apr 27, 2020 (154)
80	HGDP	ss3847479207	Apr 27, 2020 (154)
81	SGDP_PRJ	ss3879982496	Apr 27, 2020 (154)
82	KRGDB	ss3928840211	Apr 27, 2020 (154)
83	KOGIC	ss3973570714	Apr 27, 2020 (154)
84	EVA	ss3985640061	Apr 26, 2021 (155)
85	EVA	ss4017633702	Apr 26, 2021 (155)
86	TOPMED	ss4946404612	Apr 26, 2021 (155)
87	TOMMO_GENOMICS	ss5210011298	Apr 26, 2021 (155)
88	1000G_HIGH_COVERAGE	ss5293745320	Oct 16, 2022 (156)
89	EVA	ss5315684405	Oct 16, 2022 (156)
90	EVA	ss5410787676	Oct 16, 2022 (156)
91	HUGCELL_USP	ss5488108287	Oct 16, 2022 (156)
92	EVA	ss5510974653	Oct 16, 2022 (156)
93	1000G_HIGH_COVERAGE	ss5592699236	Oct 16, 2022 (156)
94	SANFORD_IMAGENETICS	ss5654775814	Oct 16, 2022 (156)
95	TOMMO_GENOMICS	ss5761891482	Oct 16, 2022 (156)
96	YY_MCH	ss5814115454	Oct 16, 2022 (156)
97	EVA	ss5839482051	Oct 16, 2022 (156)
98	EVA	ss5850731501	Oct 16, 2022 (156)
99	EVA	ss5925121083	Oct 16, 2022 (156)
100	EVA	ss5946198802	Oct 16, 2022 (156)
101	1000Genomes	NC_000013.10 - 51419623	Oct 12, 2018 (152)
102	1000Genomes_30x	NC_000013.11 - 50845487	Oct 16, 2022 (156)
103	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 51419623	Oct 12, 2018 (152)
104	Genetic variation in the Estonian population	NC_000013.10 - 51419623	Oct 12, 2018 (152)
105	The Danish reference pan genome	NC_000013.10 - 51419623	Apr 27, 2020 (154)
106	gnomAD - Genomes	NC_000013.11 - 50845487	Apr 26, 2021 (155)
107	Genome of the Netherlands Release 5	NC_000013.10 - 51419623	Apr 27, 2020 (154)
108	HGDP-CEPH-db Supplement 1	NC_000013.9 - 50317624	Apr 27, 2020 (154)
109	HapMap	NC_000013.11 - 50845487	Apr 27, 2020 (154)
110	KOREAN population from KRGDB	NC_000013.10 - 51419623	Apr 27, 2020 (154)
111	Korean Genome Project	NC_000013.11 - 50845487	Apr 27, 2020 (154)
112	Northern Sweden	NC_000013.10 - 51419623	Jul 13, 2019 (153)
113	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000013.10 - 51419623	Apr 26, 2021 (155)
114	Qatari	NC_000013.10 - 51419623	Apr 27, 2020 (154)
115	SGDP_PRJ	NC_000013.10 - 51419623	Apr 27, 2020 (154)
116	Siberian	NC_000013.10 - 51419623	Apr 27, 2020 (154)
117	8.3KJPN	NC_000013.10 - 51419623	Apr 26, 2021 (155)
118	14KJPN	NC_000013.11 - 50845487	Oct 16, 2022 (156)
119	TopMed	NC_000013.11 - 50845487	Apr 26, 2021 (155)
120	UK 10K study - Twins	NC_000013.10 - 51419623	Oct 12, 2018 (152)
121	A Vietnamese Genetic Variation Database	NC_000013.10 - 51419623	Jul 13, 2019 (153)
122	ALFA	NC_000013.11 - 50845487	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)
rs715787	Jan 18, 2001 (92)
rs784167	Oct 23, 2000 (87)
rs59747585	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
157099, ss114702952, ss118723964, ss168110518, ss169577709, ss281715940, ss286705398, ss483202459, ss825528860, ss1684920166, ss1713391830, ss3639018923, ss3639512882, ss3643001578, ss3847479207	NC_000013.9:50317623:A:G	NC_000013.11:50845486:A:G	(self)
61106917, 33952100, 24030349, 3300693, 15148550, 36017605, 13035221, 865988, 15805728, 31999476, 8525108, 67980605, 33952100, 7532912, ss226188040, ss236254442, ss242750243, ss483255558, ss535473436, ss563670870, ss659275755, ss780209210, ss782071266, ss833010130, ss835693995, ss990396108, ss1079088699, ss1348234911, ss1427189616, ss1576790622, ss1630291358, ss1673285391, ss1807612894, ss1933763798, ss1967784083, ss2027642998, ss2156008754, ss2628311342, ss2633065114, ss2700388221, ss2919686996, ss3011026389, ss3350457746, ss3627067124, ss3631068387, ss3638011901, ss3641839068, ss3678292101, ss3739750356, ss3751468481, ss3833548794, ss3840355904, ss3879982496, ss3928840211, ss3985640061, ss4017633702, ss5210011298, ss5315684405, ss5410787676, ss5510974653, ss5654775814, ss5839482051, ss5946198802	NC_000013.10:51419622:A:G	NC_000013.11:50845486:A:G	(self)
80225171, 430817225, 992127, 29948715, 95728586, 161950270, 1953994358, ss2196358885, ss3027637853, ss3650033970, ss3695298720, ss3816798957, ss3845841745, ss3973570714, ss4946404612, ss5293745320, ss5488108287, ss5592699236, ss5761891482, ss5814115454, ss5850731501, ss5925121083	NC_000013.11:50845486:A:G	NC_000013.11:50845486:A:G	(self)
ss13286102	NT_024524.12:19994114:A:G	NC_000013.11:50845486:A:G	(self)
ss54492, ss685522, ss935628, ss1861189, ss5567690, ss43542076, ss66588557, ss67385856, ss67761835, ss70829583, ss71412080, ss74929214, ss79198342, ss83361421, ss122406133, ss154322153, ss154805523, ss159498764, ss171942700, ss173839499, ss410936724	NT_024524.14:32399622:A:G	NC_000013.11:50845486: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 rs48407

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

rs48407