Name: rs28455998
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.

rs28455998

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:41138771 (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: T=0.445680 (117967/264690, TOPMED)
T=0.450156 (62650/139174, GnomAD)
A=0.31064 (8778/28258, 14KJPN) (+ 14 more)
T=0.47935 (9055/18890, ALFA)
A=0.31247 (5237/16760, 8.3KJPN)
T=0.4621 (2959/6404, 1000G_30x)
T=0.4679 (2343/5008, 1000G)
A=0.4754 (1832/3854, ALSPAC)
A=0.4690 (1739/3708, TWINSUK)
A=0.3150 (923/2930, KOREAN)
A=0.2965 (542/1828, Korea1K)
A=0.435 (434/998, GoNL)
A=0.387 (232/600, NorthernSweden)
T=0.294 (116/394, SGDP_PRJ)
T=0.421 (91/216, Qatari)
A=0.40 (16/40, GENOME_DK)
T=0.39 (15/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	T=0.47935	A=0.52065	0.246374	0.287665	0.465961	22
European	Sub	14286	T=0.52163	A=0.47837	0.278874	0.235615	0.48551	3
African	Sub	2946	T=0.2407	A=0.7593	0.057705	0.576375	0.36592	0
African Others	Sub	114	T=0.167	A=0.833	0.035088	0.701754	0.263158	0
African American	Sub	2832	T=0.2436	A=0.7564	0.058616	0.571328	0.370056	0
Asian	Sub	112	T=0.759	A=0.241	0.589286	0.071429	0.339286	0
East Asian	Sub	86	T=0.73	A=0.27	0.534884	0.069767	0.395349	0
Other Asian	Sub	26	T=0.85	A=0.15	0.769231	0.076923	0.153846	1
Latin American 1	Sub	146	T=0.493	A=0.507	0.219178	0.232877	0.547945	0
Latin American 2	Sub	610	T=0.626	A=0.374	0.393443	0.140984	0.465574	0
South Asian	Sub	98	T=0.38	A=0.62	0.102041	0.346939	0.55102	1
Other	Sub	692	T=0.460	A=0.540	0.219653	0.300578	0.479769	0

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=0.445680	A=0.554320
gnomAD - Genomes	Global	Study-wide	139174	T=0.450156	A=0.549844
gnomAD - Genomes	European	Sub	75412	T=0.53519	A=0.46481
gnomAD - Genomes	African	Sub	41756	T=0.24698	A=0.75302
gnomAD - Genomes	American	Sub	13472	T=0.53652	A=0.46348
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	T=0.4758	A=0.5242
gnomAD - Genomes	East Asian	Sub	3090	T=0.7000	A=0.3000
gnomAD - Genomes	Other	Sub	2132	T=0.4737	A=0.5263
14KJPN	JAPANESE	Study-wide	28258	T=0.68936	A=0.31064
Allele Frequency Aggregator	Total	Global	18890	T=0.47935	A=0.52065
Allele Frequency Aggregator	European	Sub	14286	T=0.52163	A=0.47837
Allele Frequency Aggregator	African	Sub	2946	T=0.2407	A=0.7593
Allele Frequency Aggregator	Other	Sub	692	T=0.460	A=0.540
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.626	A=0.374
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.493	A=0.507
Allele Frequency Aggregator	Asian	Sub	112	T=0.759	A=0.241
Allele Frequency Aggregator	South Asian	Sub	98	T=0.38	A=0.62
8.3KJPN	JAPANESE	Study-wide	16760	T=0.68753	A=0.31247
1000Genomes_30x	Global	Study-wide	6404	T=0.4621	A=0.5379
1000Genomes_30x	African	Sub	1786	T=0.2044	A=0.7956
1000Genomes_30x	Europe	Sub	1266	T=0.5095	A=0.4905
1000Genomes_30x	South Asian	Sub	1202	T=0.4542	A=0.5458
1000Genomes_30x	East Asian	Sub	1170	T=0.7145	A=0.2855
1000Genomes_30x	American	Sub	980	T=0.579	A=0.421
1000Genomes	Global	Study-wide	5008	T=0.4679	A=0.5321
1000Genomes	African	Sub	1322	T=0.2110	A=0.7890
1000Genomes	East Asian	Sub	1008	T=0.7103	A=0.2897
1000Genomes	Europe	Sub	1006	T=0.5040	A=0.4960
1000Genomes	South Asian	Sub	978	T=0.451	A=0.549
1000Genomes	American	Sub	694	T=0.576	A=0.424
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5246	A=0.4754
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5310	A=0.4690
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6850	A=0.3150
Korean Genome Project	KOREAN	Study-wide	1828	T=0.7035	A=0.2965
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.565	A=0.435
Northern Sweden	ACPOP	Study-wide	600	T=0.613	A=0.387
SGDP_PRJ	Global	Study-wide	394	T=0.294	A=0.706
Qatari	Global	Study-wide	216	T=0.421	A=0.579
The Danish reference pan genome	Danish	Study-wide	40	T=0.60	A=0.40
Siberian	Global	Study-wide	38	T=0.39	A=0.61

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 15	NC_000015.10:g.41138771T>A
GRCh37.p13 chr 15	NC_000015.9:g.41430969T>A

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 15	NC_000015.10:g.41138771=	NC_000015.10:g.41138771T>A
GRCh37.p13 chr 15	NC_000015.9:g.41430969=	NC_000015.9:g.41430969T>A

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#.

56 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35196655	May 24, 2005 (125)
2	1000GENOMES	ss108763439	Jan 23, 2009 (130)
3	ILLUMINA-UK	ss118201804	Dec 01, 2009 (131)
4	GMI	ss156461067	Dec 01, 2009 (131)
5	BUSHMAN	ss200758323	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss207396855	Jul 04, 2010 (132)
7	1000GENOMES	ss226857873	Jul 14, 2010 (132)
8	1000GENOMES	ss236754538	Jul 15, 2010 (132)
9	1000GENOMES	ss243145325	Jul 15, 2010 (132)
10	GMI	ss282228051	May 04, 2012 (137)
11	GMI	ss286940925	Apr 25, 2013 (138)
12	SSMP	ss660156010	Apr 25, 2013 (138)
13	EVA-GONL	ss991713616	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1080069873	Aug 21, 2014 (142)
15	1000GENOMES	ss1353169904	Aug 21, 2014 (142)
16	DDI	ss1427604022	Apr 01, 2015 (144)
17	EVA_GENOME_DK	ss1577576531	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1632844239	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1675838272	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1935118790	Feb 12, 2016 (147)
21	JJLAB	ss2028339109	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2156736841	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2206180635	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2628663584	Nov 08, 2017 (151)
25	GRF	ss2701203705	Nov 08, 2017 (151)
26	GNOMAD	ss2934039927	Nov 08, 2017 (151)
27	SWEGEN	ss3013162817	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3027993437	Nov 08, 2017 (151)
29	CSHL	ss3351084458	Nov 08, 2017 (151)
30	EVA_DECODE	ss3697751663	Jul 13, 2019 (153)
31	ACPOP	ss3740863533	Jul 13, 2019 (153)
32	EVA	ss3752995373	Jul 13, 2019 (153)
33	PACBIO	ss3787826300	Jul 13, 2019 (153)
34	PACBIO	ss3792841995	Jul 13, 2019 (153)
35	PACBIO	ss3797726465	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3818314833	Jul 13, 2019 (153)
37	EVA	ss3834200145	Apr 27, 2020 (154)
38	EVA	ss3840699048	Apr 27, 2020 (154)
39	EVA	ss3846187649	Apr 27, 2020 (154)
40	SGDP_PRJ	ss3882765008	Apr 27, 2020 (154)
41	KRGDB	ss3931903132	Apr 27, 2020 (154)
42	KOGIC	ss3975991745	Apr 27, 2020 (154)
43	TOPMED	ss4988734515	Apr 27, 2021 (155)
44	TOMMO_GENOMICS	ss5215842587	Apr 27, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5298184244	Oct 16, 2022 (156)
46	EVA	ss5418764276	Oct 16, 2022 (156)
47	HUGCELL_USP	ss5491942132	Oct 16, 2022 (156)
48	EVA	ss5511406431	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5599456044	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5657365660	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5769542266	Oct 16, 2022 (156)
52	YY_MCH	ss5815270109	Oct 16, 2022 (156)
53	EVA	ss5828105588	Oct 16, 2022 (156)
54	EVA	ss5851263607	Oct 16, 2022 (156)
55	EVA	ss5875583488	Oct 16, 2022 (156)
56	EVA	ss5948762391	Oct 16, 2022 (156)
57	1000Genomes	NC_000015.9 - 41430969	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000015.10 - 41138771	Oct 16, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 41430969	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000015.9 - 41430969	Apr 27, 2020 (154)
61	gnomAD - Genomes	NC_000015.10 - 41138771	Apr 27, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000015.9 - 41430969	Apr 27, 2020 (154)
63	KOREAN population from KRGDB	NC_000015.9 - 41430969	Apr 27, 2020 (154)
64	Korean Genome Project	NC_000015.10 - 41138771	Apr 27, 2020 (154)
65	Northern Sweden	NC_000015.9 - 41430969	Jul 13, 2019 (153)
66	Qatari	NC_000015.9 - 41430969	Apr 27, 2020 (154)
67	SGDP_PRJ	NC_000015.9 - 41430969	Apr 27, 2020 (154)
68	Siberian	NC_000015.9 - 41430969	Apr 27, 2020 (154)
69	8.3KJPN	NC_000015.9 - 41430969	Apr 27, 2021 (155)
70	14KJPN	NC_000015.10 - 41138771	Oct 16, 2022 (156)
71	TopMed	NC_000015.10 - 41138771	Apr 27, 2021 (155)
72	UK 10K study - Twins	NC_000015.9 - 41430969	Oct 12, 2018 (152)
73	ALFA	NC_000015.10 - 41138771	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35196655, ss108763439, ss118201804, ss200758323, ss207396855, ss282228051, ss286940925	NC_000015.8:39218260:T:A	NC_000015.10:41138770:T:A	(self)
66231025, 36767571, 3829138, 16424258, 39080526, 14148398, 17160720, 34781988, 9253195, 73811894, 36767571, ss226857873, ss236754538, ss243145325, ss660156010, ss991713616, ss1080069873, ss1353169904, ss1427604022, ss1577576531, ss1632844239, ss1675838272, ss1935118790, ss2028339109, ss2156736841, ss2628663584, ss2701203705, ss2934039927, ss3013162817, ss3351084458, ss3740863533, ss3752995373, ss3787826300, ss3792841995, ss3797726465, ss3834200145, ss3840699048, ss3882765008, ss3931903132, ss5215842587, ss5418764276, ss5511406431, ss5657365660, ss5828105588, ss5948762391	NC_000015.9:41430968:T:A	NC_000015.10:41138770:T:A	(self)
86981979, 466863944, 32369746, 103379370, 204280175, 4921522785, ss2206180635, ss3027993437, ss3697751663, ss3818314833, ss3846187649, ss3975991745, ss4988734515, ss5298184244, ss5491942132, ss5599456044, ss5769542266, ss5815270109, ss5851263607, ss5875583488	NC_000015.10:41138770:T:A	NC_000015.10:41138770:T:A	(self)
ss156461067	NT_010194.17:12221525:T:A	NC_000015.10:41138770: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 rs28455998

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
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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

rs28455998