Name: rs4984484
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.

rs4984484

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:96055426 (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 / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.436163 (115448/264690, TOPMED)
C=0.436734 (61141/139996, GnomAD)
C=0.26400 (7460/28258, 14KJPN) (+ 16 more)
C=0.43552 (8227/18890, ALFA)
C=0.26158 (4384/16760, 8.3KJPN)
C=0.4279 (2740/6404, 1000G_30x)
C=0.4295 (2151/5008, 1000G)
C=0.4277 (1916/4480, Estonian)
C=0.4232 (1631/3854, ALSPAC)
C=0.4299 (1594/3708, TWINSUK)
C=0.3290 (964/2930, KOREAN)
C=0.422 (421/998, GoNL)
C=0.443 (266/600, NorthernSweden)
T=0.332 (127/382, SGDP_PRJ)
C=0.404 (127/314, HapMap)
C=0.495 (107/216, Qatari)
T=0.495 (107/216, Vietnamese)
C=0.35 (14/40, GENOME_DK)
T=0.46 (11/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC112268156 : 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=0.56448	C=0.43552
European	Sub	14286	T=0.56377	C=0.43623
African	Sub	2946	T=0.5645	C=0.4355
African Others	Sub	114	T=0.518	C=0.482
African American	Sub	2832	T=0.5664	C=0.4336
Asian	Sub	112	T=0.580	C=0.420
East Asian	Sub	86	T=0.56	C=0.44
Other Asian	Sub	26	T=0.65	C=0.35
Latin American 1	Sub	146	T=0.548	C=0.452
Latin American 2	Sub	610	T=0.600	C=0.400
South Asian	Sub	98	T=0.60	C=0.40
Other	Sub	692	T=0.543	C=0.457

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=0.563837	C=0.436163
gnomAD - Genomes	Global	Study-wide	139996	T=0.563266	C=0.436734
gnomAD - Genomes	European	Sub	75846	T=0.56401	C=0.43599
gnomAD - Genomes	African	Sub	41910	T=0.55712	C=0.44288
gnomAD - Genomes	American	Sub	13640	T=0.57925	C=0.42075
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.5702	C=0.4298
gnomAD - Genomes	East Asian	Sub	3130	T=0.5601	C=0.4399
gnomAD - Genomes	Other	Sub	2150	T=0.5493	C=0.4507
14KJPN	JAPANESE	Study-wide	28258	T=0.73600	C=0.26400
Allele Frequency Aggregator	Total	Global	18890	T=0.56448	C=0.43552
Allele Frequency Aggregator	European	Sub	14286	T=0.56377	C=0.43623
Allele Frequency Aggregator	African	Sub	2946	T=0.5645	C=0.4355
Allele Frequency Aggregator	Other	Sub	692	T=0.543	C=0.457
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.600	C=0.400
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.548	C=0.452
Allele Frequency Aggregator	Asian	Sub	112	T=0.580	C=0.420
Allele Frequency Aggregator	South Asian	Sub	98	T=0.60	C=0.40
8.3KJPN	JAPANESE	Study-wide	16760	T=0.73842	C=0.26158
1000Genomes_30x	Global	Study-wide	6404	T=0.5721	C=0.4279
1000Genomes_30x	African	Sub	1786	T=0.5655	C=0.4345
1000Genomes_30x	Europe	Sub	1266	T=0.5395	C=0.4605
1000Genomes_30x	South Asian	Sub	1202	T=0.6165	C=0.3835
1000Genomes_30x	East Asian	Sub	1170	T=0.5462	C=0.4538
1000Genomes_30x	American	Sub	980	T=0.603	C=0.397
1000Genomes	Global	Study-wide	5008	T=0.5705	C=0.4295
1000Genomes	African	Sub	1322	T=0.5673	C=0.4327
1000Genomes	East Asian	Sub	1008	T=0.5446	C=0.4554
1000Genomes	Europe	Sub	1006	T=0.5358	C=0.4642
1000Genomes	South Asian	Sub	978	T=0.618	C=0.382
1000Genomes	American	Sub	694	T=0.598	C=0.402
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5723	C=0.4277
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5768	C=0.4232
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5701	C=0.4299
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6710	C=0.3290, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.578	C=0.422
Northern Sweden	ACPOP	Study-wide	600	T=0.557	C=0.443
SGDP_PRJ	Global	Study-wide	382	T=0.332	C=0.668
HapMap	Global	Study-wide	314	T=0.596	C=0.404
HapMap	African	Sub	114	T=0.553	C=0.447
HapMap	American	Sub	110	T=0.564	C=0.436
HapMap	Asian	Sub	90	T=0.69	C=0.31
Qatari	Global	Study-wide	216	T=0.505	C=0.495
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.495	C=0.505
The Danish reference pan genome	Danish	Study-wide	40	T=0.65	C=0.35
Siberian	Global	Study-wide	24	T=0.46	C=0.54

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.96055426T>A
GRCh38.p14 chr 15	NC_000015.10:g.96055426T>C
GRCh38.p14 chr 15	NC_000015.10:g.96055426T>G
GRCh37.p13 chr 15	NC_000015.9:g.96598655T>A
GRCh37.p13 chr 15	NC_000015.9:g.96598655T>C
GRCh37.p13 chr 15	NC_000015.9:g.96598655T>G

Gene: LOC112268156, uncharacterized LOC112268156 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC112268156 transcript	XR_002957737.1: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	T=	A	C	G
GRCh38.p14 chr 15	NC_000015.10:g.96055426=	NC_000015.10:g.96055426T>A	NC_000015.10:g.96055426T>C	NC_000015.10:g.96055426T>G
GRCh37.p13 chr 15	NC_000015.9:g.96598655=	NC_000015.9:g.96598655T>A	NC_000015.9:g.96598655T>C	NC_000015.9:g.96598655T>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#.

75 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6900500	Feb 20, 2003 (111)
2	SSAHASNP	ss21228849	Apr 05, 2004 (121)
3	ABI	ss40534965	Mar 15, 2006 (126)
4	HGSV	ss83915810	Dec 14, 2007 (130)
5	BCMHGSC_JDW	ss90264982	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96837013	Feb 04, 2009 (130)
7	1000GENOMES	ss109067258	Jan 23, 2009 (130)
8	ILLUMINA-UK	ss118344699	Feb 14, 2009 (130)
9	ENSEMBL	ss132441861	Dec 01, 2009 (131)
10	ENSEMBL	ss136510826	Dec 01, 2009 (131)
11	GMI	ss156903450	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss168541018	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss170329204	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss171561675	Jul 04, 2010 (132)
15	BUSHMAN	ss201231682	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207375707	Jul 04, 2010 (132)
17	1000GENOMES	ss211657904	Jul 14, 2010 (132)
18	1000GENOMES	ss227057945	Jul 14, 2010 (132)
19	1000GENOMES	ss236894099	Jul 15, 2010 (132)
20	1000GENOMES	ss243259563	Jul 15, 2010 (132)
21	GMI	ss282378028	May 04, 2012 (137)
22	GMI	ss287008601	Apr 25, 2013 (138)
23	PJP	ss291782837	May 09, 2011 (134)
24	TISHKOFF	ss564676398	Apr 25, 2013 (138)
25	SSMP	ss660419402	Apr 25, 2013 (138)
26	EVA-GONL	ss992120480	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1080369421	Aug 21, 2014 (142)
28	1000GENOMES	ss1354757721	Aug 21, 2014 (142)
29	DDI	ss1427728298	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1577768343	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1633690364	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1676684397	Apr 01, 2015 (144)
33	EVA_DECODE	ss1696151823	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1808346909	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1935523587	Feb 12, 2016 (147)
36	GENOMED	ss1968183553	Jul 19, 2016 (147)
37	JJLAB	ss2028546593	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2156955586	Nov 08, 2017 (151)
39	HUMAN_LONGEVITY	ss2209398684	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2628768489	Nov 08, 2017 (151)
41	GRF	ss2701444899	Nov 08, 2017 (151)
42	GNOMAD	ss2938591700	Nov 08, 2017 (151)
43	SWEGEN	ss3013810555	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3028098067	Nov 08, 2017 (151)
45	CSHL	ss3351260380	Nov 08, 2017 (151)
46	URBANLAB	ss3650426665	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3680942880	Jul 13, 2019 (153)
48	EVA_DECODE	ss3698532337	Jul 13, 2019 (153)
49	ACPOP	ss3741201097	Jul 13, 2019 (153)
50	EVA	ss3753490471	Jul 13, 2019 (153)
51	PACBIO	ss3787937188	Jul 13, 2019 (153)
52	PACBIO	ss3792934982	Jul 13, 2019 (153)
53	PACBIO	ss3797819649	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3818792238	Jul 13, 2019 (153)
55	EVA	ss3834395450	Apr 27, 2020 (154)
56	EVA	ss3840801303	Apr 27, 2020 (154)
57	EVA	ss3846291623	Apr 27, 2020 (154)
58	SGDP_PRJ	ss3883599878	Apr 27, 2020 (154)
59	KRGDB	ss3932858612	Apr 27, 2020 (154)
60	KOGIC	ss3976809132	Apr 27, 2020 (154)
61	KOGIC	ss3976809133	Apr 27, 2020 (154)
62	TOPMED	ss5002664987	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5217703936	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5299581867	Oct 16, 2022 (156)
65	EVA	ss5421318668	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5493181121	Oct 16, 2022 (156)
67	EVA	ss5511529303	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5601550322	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5658151762	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5771964788	Oct 16, 2022 (156)
71	YY_MCH	ss5815619526	Oct 16, 2022 (156)
72	EVA	ss5828641746	Oct 16, 2022 (156)
73	EVA	ss5851425963	Oct 16, 2022 (156)
74	EVA	ss5877179578	Oct 16, 2022 (156)
75	EVA	ss5949579507	Oct 16, 2022 (156)
76	1000Genomes	NC_000015.9 - 96598655	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000015.10 - 96055426	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 96598655	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000015.9 - 96598655	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000015.9 - 96598655	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000015.10 - 96055426	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000015.9 - 96598655	Apr 27, 2020 (154)
83	HapMap	NC_000015.10 - 96055426	Apr 27, 2020 (154)
84	KOREAN population from KRGDB	NC_000015.9 - 96598655	Apr 27, 2020 (154)
85	Korean Genome Project Submission ignored due to conflicting rows: Row 33187133 (NC_000015.10:96055425:T:C 582/1832) Row 33187134 (NC_000015.10:96055425:T:A 1/1832)	-	Apr 27, 2020 (154)
86	Korean Genome Project Submission ignored due to conflicting rows: Row 33187133 (NC_000015.10:96055425:T:C 582/1832) Row 33187134 (NC_000015.10:96055425:T:A 1/1832)	-	Apr 27, 2020 (154)
87	Northern Sweden	NC_000015.9 - 96598655	Jul 13, 2019 (153)
88	Qatari	NC_000015.9 - 96598655	Apr 27, 2020 (154)
89	SGDP_PRJ	NC_000015.9 - 96598655	Apr 27, 2020 (154)
90	Siberian	NC_000015.9 - 96598655	Apr 27, 2020 (154)
91	8.3KJPN	NC_000015.9 - 96598655	Apr 26, 2021 (155)
92	14KJPN	NC_000015.10 - 96055426	Oct 16, 2022 (156)
93	TopMed	NC_000015.10 - 96055426	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000015.9 - 96598655	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000015.9 - 96598655	Jul 13, 2019 (153)
96	ALFA	NC_000015.10 - 96055426	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)
rs57652729	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3976809133	NC_000015.10:96055425:T:A	NC_000015.10:96055425:T:A	(self)
ss83915810, ss90264982, ss109067258, ss118344699, ss168541018, ss170329204, ss171561675, ss201231682, ss207375707, ss211657904, ss282378028, ss287008601, ss291782837, ss1696151823	NC_000015.8:94399658:T:C	NC_000015.10:96055425:T:C	(self)
67875382, 37697588, 26681128, 3986698, 16818841, 40036006, 14485962, 17565509, 35616858, 9471940, 75673243, 37697588, 8379377, ss227057945, ss236894099, ss243259563, ss564676398, ss660419402, ss992120480, ss1080369421, ss1354757721, ss1427728298, ss1577768343, ss1633690364, ss1676684397, ss1808346909, ss1935523587, ss1968183553, ss2028546593, ss2156955586, ss2628768489, ss2701444899, ss2938591700, ss3013810555, ss3351260380, ss3680942880, ss3741201097, ss3753490471, ss3787937188, ss3792934982, ss3797819649, ss3834395450, ss3840801303, ss3883599878, ss3932858612, ss5217703936, ss5421318668, ss5511529303, ss5658151762, ss5828641746, ss5949579507	NC_000015.9:96598654:T:C	NC_000015.10:96055425:T:C	(self)
89076257, 478481314, 1323735, 105801892, 218210647, 7395853427, ss2209398684, ss3028098067, ss3650426665, ss3698532337, ss3818792238, ss3846291623, ss3976809132, ss5002664987, ss5299581867, ss5493181121, ss5601550322, ss5771964788, ss5815619526, ss5851425963, ss5877179578	NC_000015.10:96055425:T:C	NC_000015.10:96055425:T:C	(self)
ss21228849	NT_010274.15:11564181:T:C	NC_000015.10:96055425:T:C	(self)
ss6900500, ss40534965, ss96837013, ss132441861, ss136510826, ss156903450	NT_010274.17:11564181:T:C	NC_000015.10:96055425:T:C	(self)
40036006, ss3932858612	NC_000015.9:96598654:T:G	NC_000015.10:96055425:T: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 rs4984484

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

rs4984484