Name: rs7990354
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.

rs7990354

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28539454 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.004908 (1299/264690, TOPMED)
C=0.004694 (658/140184, GnomAD)
C=0.00071 (20/28256, 14KJPN) (+ 15 more)
C=0.00308 (57/18520, ALFA)
C=0.00078 (13/16758, 8.3KJPN)
C=0.0061 (39/6404, 1000G_30x)
C=0.0062 (31/5008, 1000G)
C=0.0013 (6/4480, Estonian)
C=0.0013 (5/3854, ALSPAC)
C=0.0024 (9/3708, TWINSUK)
C=0.0024 (7/2928, KOREAN)
C=0.0005 (1/1832, Korea1K)
C=0.001 (1/998, GoNL)
C=0.000 (0/600, NorthernSweden)
C=0.009 (5/558, SGDP_PRJ)
C=0.000 (0/216, Qatari)
C=0.00 (0/40, GENOME_DK)
C=0.00 (0/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124903142 : 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	18520	C=0.00308	T=0.99692
European	Sub	14152	C=0.00120	T=0.99880
African	Sub	2898	C=0.0117	T=0.9883
African Others	Sub	114	C=0.035	T=0.965
African American	Sub	2784	C=0.0108	T=0.9892
Asian	Sub	112	C=0.009	T=0.991
East Asian	Sub	86	C=0.01	T=0.99
Other Asian	Sub	26	C=0.00	T=1.00
Latin American 1	Sub	146	C=0.014	T=0.986
Latin American 2	Sub	610	C=0.000	T=1.000
South Asian	Sub	98	C=0.00	T=1.00
Other	Sub	504	C=0.006	T=0.994

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=0.004908	T=0.995092
gnomAD - Genomes	Global	Study-wide	140184	C=0.004694	T=0.995306
gnomAD - Genomes	European	Sub	75928	C=0.00113	T=0.99887
gnomAD - Genomes	African	Sub	41990	C=0.01262	T=0.98738
gnomAD - Genomes	American	Sub	13658	C=0.00234	T=0.99766
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0000	T=1.0000
gnomAD - Genomes	East Asian	Sub	3132	C=0.0003	T=0.9997
gnomAD - Genomes	Other	Sub	2152	C=0.0042	T=0.9958
14KJPN	JAPANESE	Study-wide	28256	C=0.00071	T=0.99929
Allele Frequency Aggregator	Total	Global	18520	C=0.00308	T=0.99692
Allele Frequency Aggregator	European	Sub	14152	C=0.00120	T=0.99880
Allele Frequency Aggregator	African	Sub	2898	C=0.0117	T=0.9883
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.000	T=1.000
Allele Frequency Aggregator	Other	Sub	504	C=0.006	T=0.994
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.014	T=0.986
Allele Frequency Aggregator	Asian	Sub	112	C=0.009	T=0.991
Allele Frequency Aggregator	South Asian	Sub	98	C=0.00	T=1.00
8.3KJPN	JAPANESE	Study-wide	16758	C=0.00078	T=0.99922
1000Genomes_30x	Global	Study-wide	6404	C=0.0061	T=0.9939
1000Genomes_30x	African	Sub	1786	C=0.0207	T=0.9793
1000Genomes_30x	Europe	Sub	1266	C=0.0008	T=0.9992
1000Genomes_30x	South Asian	Sub	1202	C=0.0000	T=1.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0009	T=0.9991
1000Genomes_30x	American	Sub	980	C=0.000	T=1.000
1000Genomes	Global	Study-wide	5008	C=0.0062	T=0.9938
1000Genomes	African	Sub	1322	C=0.0219	T=0.9781
1000Genomes	East Asian	Sub	1008	C=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	C=0.0020	T=0.9980
1000Genomes	South Asian	Sub	978	C=0.000	T=1.000
1000Genomes	American	Sub	694	C=0.000	T=1.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.0013	T=0.9987
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0013	T=0.9987
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0024	T=0.9976
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.0024	T=0.9976
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0005	T=0.9995
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.001	T=0.999
Northern Sweden	ACPOP	Study-wide	600	C=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	C=0.009	T=0.991
Qatari	Global	Study-wide	216	C=0.000	T=1.000
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	T=1.00
Siberian	Global	Study-wide	12	C=0.00	T=1.00

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.28539454C>T
GRCh37.p13 chr 13	NC_000013.10:g.29113591C>T

Gene: LOC124903142, uncharacterized LOC124903142 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903142 transcript	XR_007063737.1: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	C=	T
GRCh38.p14 chr 13	NC_000013.11:g.28539454=	NC_000013.11:g.28539454C>T
GRCh37.p13 chr 13	NC_000013.10:g.29113591=	NC_000013.10:g.29113591C>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#.

68 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss12245791	Jul 11, 2003 (116)
2	SC_SNP	ss13157394	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss17498950	Feb 27, 2004 (120)
4	SSAHASNP	ss21124183	Apr 05, 2004 (121)
5	HGSV	ss78853815	Dec 07, 2007 (129)
6	HGSV	ss82392098	Dec 14, 2007 (130)
7	BCMHGSC_JDW	ss89558152	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss96954626	Feb 04, 2009 (130)
9	ENSEMBL	ss133503865	Dec 01, 2009 (131)
10	ENSEMBL	ss137274306	Dec 01, 2009 (131)
11	GMI	ss154582679	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss167789259	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss169069318	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss170930397	Jul 04, 2010 (132)
15	BUSHMAN	ss199012164	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss206804281	Jul 04, 2010 (132)
17	BL	ss254884481	May 09, 2011 (134)
18	GMI	ss281652729	May 04, 2012 (137)
19	GMI	ss286675112	Apr 25, 2013 (138)
20	PJP	ss291564645	May 09, 2011 (134)
21	1000GENOMES	ss337782806	May 09, 2011 (134)
22	TISHKOFF	ss563571097	Apr 25, 2013 (138)
23	SSMP	ss659166904	Apr 25, 2013 (138)
24	EVA-GONL	ss990227678	Aug 21, 2014 (142)
25	1000GENOMES	ss1347617157	Aug 21, 2014 (142)
26	DDI	ss1427140194	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1576694470	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1629955735	Apr 01, 2015 (144)
29	EVA_DECODE	ss1642332313	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1672949768	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1807541385	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1933596606	Feb 12, 2016 (147)
33	USC_VALOUEV	ss2155918610	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2195097508	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2628265064	Nov 08, 2017 (151)
36	GRF	ss2700290781	Nov 08, 2017 (151)
37	GNOMAD	ss2917937305	Nov 08, 2017 (151)
38	SWEGEN	ss3010773283	Nov 08, 2017 (151)
39	CSHL	ss3350381577	Nov 08, 2017 (151)
40	URBANLAB	ss3649996263	Oct 12, 2018 (152)
41	ILLUMINA	ss3651879687	Oct 12, 2018 (152)
42	EGCUT_WGS	ss3678034041	Jul 13, 2019 (153)
43	EVA_DECODE	ss3694990379	Jul 13, 2019 (153)
44	ACPOP	ss3739611798	Jul 13, 2019 (153)
45	EVA	ss3751274993	Jul 13, 2019 (153)
46	PACBIO	ss3787414076	Jul 13, 2019 (153)
47	PACBIO	ss3792486760	Jul 13, 2019 (153)
48	PACBIO	ss3797370477	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3816606006	Jul 13, 2019 (153)
50	EVA	ss3833466526	Apr 27, 2020 (154)
51	EVA	ss3840310376	Apr 27, 2020 (154)
52	EVA	ss3845795108	Apr 27, 2020 (154)
53	SGDP_PRJ	ss3879659467	Apr 27, 2020 (154)
54	KRGDB	ss3928480792	Apr 27, 2020 (154)
55	KOGIC	ss3973266907	Apr 27, 2020 (154)
56	TOPMED	ss4940976929	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5209313832	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5293206246	Oct 16, 2022 (156)
59	EVA	ss5409801492	Oct 16, 2022 (156)
60	HUGCELL_USP	ss5487622413	Oct 16, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5591889914	Oct 16, 2022 (156)
62	SANFORD_IMAGENETICS	ss5654465281	Oct 16, 2022 (156)
63	TOMMO_GENOMICS	ss5760994676	Oct 16, 2022 (156)
64	YY_MCH	ss5813978280	Oct 16, 2022 (156)
65	EVA	ss5839265858	Oct 16, 2022 (156)
66	EVA	ss5850661621	Oct 16, 2022 (156)
67	EVA	ss5924494691	Oct 16, 2022 (156)
68	EVA	ss5945871537	Oct 16, 2022 (156)
69	1000Genomes	NC_000013.10 - 29113591	Oct 12, 2018 (152)
70	1000Genomes_30x	NC_000013.11 - 28539454	Oct 16, 2022 (156)
71	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29113591	Oct 12, 2018 (152)
72	Genetic variation in the Estonian population	NC_000013.10 - 29113591	Oct 12, 2018 (152)
73	The Danish reference pan genome	NC_000013.10 - 29113591	Apr 27, 2020 (154)
74	gnomAD - Genomes	NC_000013.11 - 28539454	Apr 26, 2021 (155)
75	Genome of the Netherlands Release 5	NC_000013.10 - 29113591	Apr 27, 2020 (154)
76	KOREAN population from KRGDB	NC_000013.10 - 29113591	Apr 27, 2020 (154)
77	Korean Genome Project	NC_000013.11 - 28539454	Apr 27, 2020 (154)
78	Northern Sweden	NC_000013.10 - 29113591	Jul 13, 2019 (153)
79	Qatari	NC_000013.10 - 29113591	Apr 27, 2020 (154)
80	SGDP_PRJ	NC_000013.10 - 29113591	Apr 27, 2020 (154)
81	Siberian	NC_000013.10 - 29113591	Apr 27, 2020 (154)
82	8.3KJPN	NC_000013.10 - 29113591	Apr 26, 2021 (155)
83	14KJPN	NC_000013.11 - 28539454	Oct 16, 2022 (156)
84	TopMed	NC_000013.11 - 28539454	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000013.10 - 29113591	Oct 12, 2018 (152)
86	ALFA	NC_000013.11 - 28539454	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)
rs57869681	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78853815, ss82392098, ss89558152, ss167789259, ss169069318, ss170930397, ss199012164, ss206804281, ss254884481, ss281652729, ss286675112, ss291564645, ss1642332313	NC_000013.9:28011590:C:T	NC_000013.11:28539453:C:T	(self)
60465482, 33582422, 23772289, 3234098, 14984167, 35658186, 12896663, 15638536, 31676447, 8434964, 67283139, 33582422, ss337782806, ss563571097, ss659166904, ss990227678, ss1347617157, ss1427140194, ss1576694470, ss1629955735, ss1672949768, ss1807541385, ss1933596606, ss2155918610, ss2628265064, ss2700290781, ss2917937305, ss3010773283, ss3350381577, ss3651879687, ss3678034041, ss3739611798, ss3751274993, ss3787414076, ss3792486760, ss3797370477, ss3833466526, ss3840310376, ss3879659467, ss3928480792, ss5209313832, ss5409801492, ss5654465281, ss5839265858, ss5945871537	NC_000013.10:29113590:C:T	NC_000013.11:28539453:C:T	(self)
79415849, 426367026, 29644908, 94831780, 156522587, 6172936576, ss2195097508, ss3649996263, ss3694990379, ss3816606006, ss3845795108, ss3973266907, ss4940976929, ss5293206246, ss5487622413, ss5591889914, ss5760994676, ss5813978280, ss5850661621, ss5924494691	NC_000013.11:28539453:C:T	NC_000013.11:28539453:C:T	(self)
ss12245791, ss13157394	NT_009799.12:10093590:C:T	NC_000013.11:28539453:C:T	(self)
ss17498950, ss21124183	NT_024524.13:10093590:C:T	NC_000013.11:28539453:C:T	(self)
ss96954626, ss133503865, ss137274306, ss154582679	NT_024524.14:10093590:C:T	NC_000013.11:28539453: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 rs7990354

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

rs7990354