Name: rs149889
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.

rs149889

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:50491718 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.255503 (67629/264690, TOPMED)
T=0.263296 (36872/140040, GnomAD)
T=0.15482 (4375/28258, 14KJPN) (+ 16 more)
T=0.25299 (4779/18890, ALFA)
T=0.15274 (2560/16760, 8.3KJPN)
T=0.2274 (1456/6404, 1000G_30x)
T=0.2220 (1112/5008, 1000G)
T=0.2500 (1120/4480, Estonian)
T=0.2602 (1003/3854, ALSPAC)
T=0.2503 (928/3708, TWINSUK)
T=0.1369 (401/2930, KOREAN)
T=0.1332 (244/1832, Korea1K)
T=0.216 (216/998, GoNL)
T=0.300 (180/600, NorthernSweden)
T=0.147 (76/518, SGDP_PRJ)
T=0.213 (46/216, Qatari)
T=0.149 (31/208, Vietnamese)
T=0.17 (9/52, Siberian)
T=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DLEU1 : Intron Variant
LOC107984567 : 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=0.25299	C=0.74701
European	Sub	14286	T=0.25017	C=0.74983
African	Sub	2946	T=0.2889	C=0.7111
African Others	Sub	114	T=0.307	C=0.693
African American	Sub	2832	T=0.2881	C=0.7119
Asian	Sub	112	T=0.089	C=0.911
East Asian	Sub	86	T=0.09	C=0.91
Other Asian	Sub	26	T=0.08	C=0.92
Latin American 1	Sub	146	T=0.274	C=0.726
Latin American 2	Sub	610	T=0.213	C=0.787
South Asian	Sub	98	T=0.15	C=0.85
Other	Sub	692	T=0.230	C=0.770

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=0.255503	C=0.744497
gnomAD - Genomes	Global	Study-wide	140040	T=0.263296	C=0.736704
gnomAD - Genomes	European	Sub	75864	T=0.26073	C=0.73927
gnomAD - Genomes	African	Sub	41940	T=0.29509	C=0.70491
gnomAD - Genomes	American	Sub	13640	T=0.22163	C=0.77837
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.2196	C=0.7804
gnomAD - Genomes	East Asian	Sub	3132	T=0.1319	C=0.8681
gnomAD - Genomes	Other	Sub	2144	T=0.2570	C=0.7430
14KJPN	JAPANESE	Study-wide	28258	T=0.15482	C=0.84518
Allele Frequency Aggregator	Total	Global	18890	T=0.25299	C=0.74701
Allele Frequency Aggregator	European	Sub	14286	T=0.25017	C=0.74983
Allele Frequency Aggregator	African	Sub	2946	T=0.2889	C=0.7111
Allele Frequency Aggregator	Other	Sub	692	T=0.230	C=0.770
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.213	C=0.787
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.274	C=0.726
Allele Frequency Aggregator	Asian	Sub	112	T=0.089	C=0.911
Allele Frequency Aggregator	South Asian	Sub	98	T=0.15	C=0.85
8.3KJPN	JAPANESE	Study-wide	16760	T=0.15274	C=0.84726
1000Genomes_30x	Global	Study-wide	6404	T=0.2274	C=0.7726
1000Genomes_30x	African	Sub	1786	T=0.3309	C=0.6691
1000Genomes_30x	Europe	Sub	1266	T=0.2433	C=0.7567
1000Genomes_30x	South Asian	Sub	1202	T=0.1547	C=0.8453
1000Genomes_30x	East Asian	Sub	1170	T=0.1513	C=0.8487
1000Genomes_30x	American	Sub	980	T=0.198	C=0.802
1000Genomes	Global	Study-wide	5008	T=0.2220	C=0.7780
1000Genomes	African	Sub	1322	T=0.3177	C=0.6823
1000Genomes	East Asian	Sub	1008	T=0.1498	C=0.8502
1000Genomes	Europe	Sub	1006	T=0.2435	C=0.7565
1000Genomes	South Asian	Sub	978	T=0.157	C=0.843
1000Genomes	American	Sub	694	T=0.205	C=0.795
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.2500	C=0.7500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2602	C=0.7398
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2503	C=0.7497
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1369	C=0.8631
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1332	C=0.8668
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.216	C=0.784
Northern Sweden	ACPOP	Study-wide	600	T=0.300	C=0.700
SGDP_PRJ	Global	Study-wide	518	T=0.147	C=0.853
Qatari	Global	Study-wide	216	T=0.213	C=0.787
A Vietnamese Genetic Variation Database	Global	Study-wide	208	T=0.149	C=0.851
Siberian	Global	Study-wide	52	T=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.23	C=0.78

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.50491718T>C
GRCh37.p13 chr 13	NC_000013.10:g.51065854T>C

Gene: DLEU1, deleted in lymphocytic leukemia 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DLEU1 transcript variant 3	NR_109974.1:n.	N/A	Intron Variant
DLEU1 transcript variant 2	NR_002605.2:n.	N/A	Genic Downstream Transcript Variant
DLEU1 transcript variant 1	NR_109973.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC107984567, uncharacterized LOC107984567 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984567 transcript variant X1	XR_007063797.1:n.	N/A	Intron Variant
LOC107984567 transcript variant X2	XR_007063798.1:n.	N/A	Intron Variant
LOC107984567 transcript variant X3	XR_007063799.1:n.	N/A	Intron Variant
LOC107984567 transcript variant X4	XR_007063800.1:n.	N/A	Intron Variant
LOC107984567 transcript variant X5	XR_007063801.1:n.	N/A	Intron Variant
LOC107984567 transcript variant X6	XR_007063802.1:n.	N/A	Genic 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	T=	C
GRCh38.p14 chr 13	NC_000013.11:g.50491718=	NC_000013.11:g.50491718T>C
GRCh37.p13 chr 13	NC_000013.10:g.51065854=	NC_000013.10:g.51065854T>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#.

80 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss253716	Jul 12, 2000 (79)
2	KWOK	ss265584	Jul 12, 2000 (79)
3	SC_JCM	ss795387	Aug 11, 2000 (85)
4	KWOK	ss993541	Oct 04, 2000 (86)
5	KWOK	ss1067843	Oct 05, 2000 (92)
6	KWOK	ss1941605	Oct 18, 2000 (92)
7	SC_JCM	ss2604126	Nov 09, 2000 (92)
8	SC_SNP	ss13285981	Dec 05, 2003 (119)
9	CSHL-HAPMAP	ss19285155	Feb 27, 2004 (120)
10	SSAHASNP	ss21118670	Apr 05, 2004 (121)
11	PERLEGEN	ss23326605	Sep 20, 2004 (123)
12	ABI	ss43527631	Mar 14, 2006 (126)
13	BCMHGSC_JDW	ss89667217	Mar 24, 2008 (129)
14	HUMANGENOME_JCVI	ss95764828	Feb 05, 2009 (130)
15	BGI	ss106335081	Feb 05, 2009 (130)
16	1000GENOMES	ss112779677	Jan 25, 2009 (130)
17	1000GENOMES	ss114699203	Jan 25, 2009 (130)
18	ILLUMINA-UK	ss118721861	Feb 14, 2009 (130)
19	ENSEMBL	ss133592387	Dec 01, 2009 (131)
20	ENSEMBL	ss137225437	Dec 01, 2009 (131)
21	GMI	ss154802303	Dec 01, 2009 (131)
22	COMPLETE_GENOMICS	ss168105674	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss169569401	Jul 04, 2010 (132)
24	COMPLETE_GENOMICS	ss171165443	Jul 04, 2010 (132)
25	BUSHMAN	ss199204764	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss208531649	Jul 04, 2010 (132)
27	1000GENOMES	ss226186709	Jul 14, 2010 (132)
28	1000GENOMES	ss236253434	Jul 15, 2010 (132)
29	1000GENOMES	ss242749452	Jul 15, 2010 (132)
30	GMI	ss281715015	May 04, 2012 (137)
31	GMI	ss286704947	Apr 25, 2013 (138)
32	PJP	ss291441927	May 09, 2011 (134)
33	TISHKOFF	ss563669478	Apr 25, 2013 (138)
34	SSMP	ss659274032	Apr 25, 2013 (138)
35	EVA-GONL	ss990393475	Aug 21, 2014 (142)
36	JMKIDD_LAB	ss1079086797	Aug 21, 2014 (142)
37	1000GENOMES	ss1348225674	Aug 21, 2014 (142)
38	DDI	ss1427188977	Apr 01, 2015 (144)
39	EVA_GENOME_DK	ss1576789036	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1630286260	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1673280293	Apr 01, 2015 (144)
42	EVA_DECODE	ss1684917624	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1807611853	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1933761345	Feb 12, 2016 (147)
45	GENOMED	ss1967783489	Jul 19, 2016 (147)
46	JJLAB	ss2027641562	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2156007509	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2196339780	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2628310626	Nov 08, 2017 (151)
50	GRF	ss2700386796	Nov 08, 2017 (151)
51	GNOMAD	ss2919661181	Nov 08, 2017 (151)
52	SWEGEN	ss3011022729	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3027637196	Nov 08, 2017 (151)
54	CSHL	ss3350456556	Nov 08, 2017 (151)
55	URBANLAB	ss3650033435	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3678288096	Jul 13, 2019 (153)
57	EVA_DECODE	ss3695294166	Jul 13, 2019 (153)
58	ACPOP	ss3739748381	Jul 13, 2019 (153)
59	EVA	ss3751465597	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3816795873	Jul 13, 2019 (153)
61	EVA	ss3833547483	Apr 27, 2020 (154)
62	EVA	ss3840355232	Apr 27, 2020 (154)
63	EVA	ss3845841067	Apr 27, 2020 (154)
64	SGDP_PRJ	ss3879977770	Apr 27, 2020 (154)
65	KRGDB	ss3928835052	Apr 27, 2020 (154)
66	KOGIC	ss3973566282	Apr 27, 2020 (154)
67	TOPMED	ss4946323087	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5210001233	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5293737397	Oct 16, 2022 (156)
70	HUGCELL_USP	ss5488101136	Oct 16, 2022 (156)
71	EVA	ss5510973829	Oct 16, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5592687226	Oct 16, 2022 (156)
73	SANFORD_IMAGENETICS	ss5654771300	Oct 16, 2022 (156)
74	TOMMO_GENOMICS	ss5761878608	Oct 16, 2022 (156)
75	YY_MCH	ss5814113395	Oct 16, 2022 (156)
76	EVA	ss5839478655	Oct 16, 2022 (156)
77	EVA	ss5850730440	Oct 16, 2022 (156)
78	EVA	ss5925111850	Oct 16, 2022 (156)
79	EVA	ss5946193956	Oct 16, 2022 (156)
80	EVA	ss5980791956	Oct 16, 2022 (156)
81	1000Genomes	NC_000013.10 - 51065854	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000013.11 - 50491718	Oct 16, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 51065854	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000013.10 - 51065854	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000013.10 - 51065854	Apr 27, 2020 (154)
86	gnomAD - Genomes	NC_000013.11 - 50491718	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000013.10 - 51065854	Apr 27, 2020 (154)
88	KOREAN population from KRGDB	NC_000013.10 - 51065854	Apr 27, 2020 (154)
89	Korean Genome Project	NC_000013.11 - 50491718	Apr 27, 2020 (154)
90	Northern Sweden	NC_000013.10 - 51065854	Jul 13, 2019 (153)
91	Qatari	NC_000013.10 - 51065854	Apr 27, 2020 (154)
92	SGDP_PRJ	NC_000013.10 - 51065854	Apr 27, 2020 (154)
93	Siberian	NC_000013.10 - 51065854	Apr 27, 2020 (154)
94	8.3KJPN	NC_000013.10 - 51065854	Apr 26, 2021 (155)
95	14KJPN	NC_000013.11 - 50491718	Oct 16, 2022 (156)
96	TopMed	NC_000013.11 - 50491718	Apr 26, 2021 (155)
97	UK 10K study - Twins	NC_000013.10 - 51065854	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000013.10 - 51065854	Jul 13, 2019 (153)
99	ALFA	NC_000013.11 - 50491718	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)
rs622960	Sep 19, 2000 (85)
rs813985	Jan 18, 2001 (92)
rs1262784	Jan 18, 2001 (92)
rs1753647	Jan 18, 2001 (92)
rs17074454	Oct 08, 2004 (123)
rs34653465	May 23, 2006 (127)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss89667217, ss112779677, ss114699203, ss118721861, ss168105674, ss169569401, ss171165443, ss199204764, ss208531649, ss281715015, ss286704947, ss291441927, ss1684917624	NC_000013.9:49963854:T:C	NC_000013.11:50491717:T:C	(self)
61097358, 33946512, 24026344, 3299755, 15145967, 36012446, 13033246, 15803275, 31994750, 8523863, 67970540, 33946512, 7531595, ss226186709, ss236253434, ss242749452, ss563669478, ss659274032, ss990393475, ss1079086797, ss1348225674, ss1427188977, ss1576789036, ss1630286260, ss1673280293, ss1807611853, ss1933761345, ss1967783489, ss2027641562, ss2156007509, ss2628310626, ss2700386796, ss2919661181, ss3011022729, ss3350456556, ss3678288096, ss3739748381, ss3751465597, ss3833547483, ss3840355232, ss3879977770, ss3928835052, ss5210001233, ss5510973829, ss5654771300, ss5839478655, ss5946193956, ss5980791956	NC_000013.10:51065853:T:C	NC_000013.11:50491717:T:C	(self)
80213161, 430751895, 29944283, 95715712, 161868745, 2298032895, ss2196339780, ss3027637196, ss3650033435, ss3695294166, ss3816795873, ss3845841067, ss3973566282, ss4946323087, ss5293737397, ss5488101136, ss5592687226, ss5761878608, ss5814113395, ss5850730440, ss5925111850	NC_000013.11:50491717:T:C	NC_000013.11:50491717:T:C	(self)
ss13285981	NT_024524.12:19640345:T:C	NC_000013.11:50491717:T:C	(self)
ss19285155, ss21118670	NT_024524.13:32045854:T:C	NC_000013.11:50491717:T:C	(self)
ss253716, ss265584, ss795387, ss993541, ss1067843, ss1941605, ss2604126, ss23326605, ss43527631, ss95764828, ss106335081, ss133592387, ss137225437, ss154802303	NT_024524.14:32045853:T:C	NC_000013.11:50491717:T:C	(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 rs149889

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

rs149889