Name: rs28362761
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.

rs28362761

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:86953728 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.094733 (25075/264690, TOPMED)
T=0.096000 (13455/140156, GnomAD)
T=0.00007 (2/28258, 14KJPN) (+ 14 more)
T=0.09280 (1753/18890, ALFA)
T=0.0823 (527/6404, 1000G_30x)
T=0.0803 (402/5008, 1000G)
T=0.0830 (372/4480, Estonian)
T=0.0960 (370/3854, ALSPAC)
T=0.1022 (379/3708, TWINSUK)
T=0.0007 (2/2922, KOREAN)
T=0.082 (82/998, GoNL)
T=0.083 (50/600, NorthernSweden)
T=0.046 (10/216, Qatari)
A=0.44 (23/52, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
A=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ELAPOR2 : 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	A=0.90720	T=0.09280
European	Sub	14286	A=0.91180	T=0.08820
African	Sub	2946	A=0.8771	T=0.1229
African Others	Sub	114	A=0.833	T=0.167
African American	Sub	2832	A=0.8789	T=0.1211
Asian	Sub	112	A=1.000	T=0.000
East Asian	Sub	86	A=1.00	T=0.00
Other Asian	Sub	26	A=1.00	T=0.00
Latin American 1	Sub	146	A=0.904	T=0.096
Latin American 2	Sub	610	A=0.936	T=0.064
South Asian	Sub	98	A=0.96	T=0.04
Other	Sub	692	A=0.893	T=0.107

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.905267	T=0.094733
gnomAD - Genomes	Global	Study-wide	140156	A=0.904000	T=0.096000
gnomAD - Genomes	European	Sub	75916	A=0.91385	T=0.08615
gnomAD - Genomes	African	Sub	41994	A=0.86924	T=0.13076
gnomAD - Genomes	American	Sub	13650	A=0.93011	T=0.06989
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9212	T=0.0788
gnomAD - Genomes	East Asian	Sub	3122	A=0.9984	T=0.0016
gnomAD - Genomes	Other	Sub	2150	A=0.9056	T=0.0944
14KJPN	JAPANESE	Study-wide	28258	A=0.99993	T=0.00007
Allele Frequency Aggregator	Total	Global	18890	A=0.90720	T=0.09280
Allele Frequency Aggregator	European	Sub	14286	A=0.91180	T=0.08820
Allele Frequency Aggregator	African	Sub	2946	A=0.8771	T=0.1229
Allele Frequency Aggregator	Other	Sub	692	A=0.893	T=0.107
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.936	T=0.064
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.904	T=0.096
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=0.96	T=0.04
1000Genomes_30x	Global	Study-wide	6404	A=0.9177	T=0.0823
1000Genomes_30x	African	Sub	1786	A=0.8583	T=0.1417
1000Genomes_30x	Europe	Sub	1266	A=0.9155	T=0.0845
1000Genomes_30x	South Asian	Sub	1202	A=0.9143	T=0.0857
1000Genomes_30x	East Asian	Sub	1170	A=0.9974	T=0.0026
1000Genomes_30x	American	Sub	980	A=0.938	T=0.062
1000Genomes	Global	Study-wide	5008	A=0.9197	T=0.0803
1000Genomes	African	Sub	1322	A=0.8578	T=0.1422
1000Genomes	East Asian	Sub	1008	A=0.9970	T=0.0030
1000Genomes	Europe	Sub	1006	A=0.9205	T=0.0795
1000Genomes	South Asian	Sub	978	A=0.911	T=0.089
1000Genomes	American	Sub	694	A=0.937	T=0.063
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9170	T=0.0830
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9040	T=0.0960
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8978	T=0.1022
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9993	T=0.0007
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.918	T=0.082
Northern Sweden	ACPOP	Study-wide	600	A=0.917	T=0.083
Qatari	Global	Study-wide	216	A=0.954	T=0.046
SGDP_PRJ	Global	Study-wide	52	A=0.44	T=0.56
The Danish reference pan genome	Danish	Study-wide	40	A=0.85	T=0.15
Siberian	Global	Study-wide	4	A=0.5	T=0.5

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 7	NC_000007.14:g.86953728A>T
GRCh37.p13 chr 7	NC_000007.13:g.86583044A>T

Gene: ELAPOR2, endosome-lysosome associated apoptosis and autophagy regulator family member 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ELAPOR2 transcript variant 1	NM_001142749.3:c.311-5806… NM_001142749.3:c.311-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant 3	NM_001291990.1:c.-32-5806… NM_001291990.1:c.-32-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant 4	NM_001291991.2:c.-248-868… NM_001291991.2:c.-248-8682T>A	N/A	Intron Variant
ELAPOR2 transcript variant 2	NM_152748.4:c.6-8682T>A	N/A	Intron Variant
ELAPOR2 transcript variant X4	XM_006715894.4:c.-32-5806… XM_006715894.4:c.-32-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X2	XM_011515918.3:c.146-5806… XM_011515918.3:c.146-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X6	XM_011515921.2:c.-32-5806… XM_011515921.2:c.-32-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X3	XM_017011843.2:c.311-5806… XM_017011843.2:c.311-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X1	XM_047420041.1:c.311-5806… XM_047420041.1:c.311-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X5	XM_047420042.1:c.-32-5806… XM_047420042.1:c.-32-5806T>A	N/A	Intron Variant
ELAPOR2 transcript variant X7	XM_024446686.2:c.	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	A=	T
GRCh38.p14 chr 7	NC_000007.14:g.86953728=	NC_000007.14:g.86953728A>T
GRCh37.p13 chr 7	NC_000007.13:g.86583044=	NC_000007.13:g.86583044A>T
KIAA1324L transcript variant 1	NM_001142749.2:c.311-5806=	NM_001142749.2:c.311-5806T>A
ELAPOR2 transcript variant 1	NM_001142749.3:c.311-5806=	NM_001142749.3:c.311-5806T>A
ELAPOR2 transcript variant 3	NM_001291990.1:c.-32-5806=	NM_001291990.1:c.-32-5806T>A
ELAPOR2 transcript variant 4	NM_001291991.2:c.-248-8682=	NM_001291991.2:c.-248-8682T>A
KIAA1324L transcript variant 2	NM_152748.3:c.6-8682=	NM_152748.3:c.6-8682T>A
ELAPOR2 transcript variant 2	NM_152748.4:c.6-8682=	NM_152748.4:c.6-8682T>A
ELAPOR2 transcript variant X4	XM_006715894.4:c.-32-5806=	XM_006715894.4:c.-32-5806T>A
ELAPOR2 transcript variant X2	XM_011515918.3:c.146-5806=	XM_011515918.3:c.146-5806T>A
ELAPOR2 transcript variant X6	XM_011515921.2:c.-32-5806=	XM_011515921.2:c.-32-5806T>A
ELAPOR2 transcript variant X3	XM_017011843.2:c.311-5806=	XM_017011843.2:c.311-5806T>A
ELAPOR2 transcript variant X1	XM_047420041.1:c.311-5806=	XM_047420041.1:c.311-5806T>A
ELAPOR2 transcript variant X5	XM_047420042.1:c.-32-5806=	XM_047420042.1:c.-32-5806T>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#.

45 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35078022	May 24, 2005 (125)
2	1000GENOMES	ss114047589	Jan 25, 2009 (130)
3	ILLUMINA-UK	ss116179384	Feb 14, 2009 (130)
4	COMPLETE_GENOMICS	ss164766487	Jul 04, 2010 (132)
5	1000GENOMES	ss223185791	Jul 14, 2010 (132)
6	1000GENOMES	ss234062483	Jul 15, 2010 (132)
7	1000GENOMES	ss241000951	Jul 15, 2010 (132)
8	TISHKOFF	ss560132249	Apr 25, 2013 (138)
9	EVA-GONL	ss984502877	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1074768617	Aug 21, 2014 (142)
11	1000GENOMES	ss1325999242	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1582292503	Apr 01, 2015 (144)
13	EVA_DECODE	ss1594078884	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1618622295	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1661616328	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1927765939	Feb 12, 2016 (147)
17	JJLAB	ss2024565488	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2152786327	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2295500452	Dec 20, 2016 (150)
20	GRF	ss2708490813	Nov 08, 2017 (151)
21	GNOMAD	ss2855771680	Nov 08, 2017 (151)
22	SWEGEN	ss3001571439	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3026076292	Nov 08, 2017 (151)
24	CSHL	ss3347715663	Nov 08, 2017 (151)
25	EGCUT_WGS	ss3669324519	Jul 13, 2019 (153)
26	EVA_DECODE	ss3720139469	Jul 13, 2019 (153)
27	ACPOP	ss3734831205	Jul 13, 2019 (153)
28	EVA	ss3766824031	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3809997025	Jul 13, 2019 (153)
30	EVA	ss3830684036	Apr 26, 2020 (154)
31	EVA	ss3838839570	Apr 26, 2020 (154)
32	EVA	ss3844294325	Apr 26, 2020 (154)
33	SGDP_PRJ	ss3867808503	Apr 26, 2020 (154)
34	KRGDB	ss3915068116	Apr 26, 2020 (154)
35	TOPMED	ss4753499914	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5273733992	Oct 13, 2022 (156)
37	EVA	ss5374957448	Oct 13, 2022 (156)
38	HUGCELL_USP	ss5470734794	Oct 13, 2022 (156)
39	EVA	ss5509035002	Oct 13, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5562357926	Oct 13, 2022 (156)
41	SANFORD_IMAGENETICS	ss5643421028	Oct 13, 2022 (156)
42	TOMMO_GENOMICS	ss5724863842	Oct 13, 2022 (156)
43	EVA	ss5823142776	Oct 13, 2022 (156)
44	EVA	ss5859748318	Oct 13, 2022 (156)
45	EVA	ss5972597266	Oct 13, 2022 (156)
46	1000Genomes	NC_000007.13 - 86583044	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000007.14 - 86953728	Oct 13, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 86583044	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000007.13 - 86583044	Oct 12, 2018 (152)
50	The Danish reference pan genome	NC_000007.13 - 86583044	Apr 26, 2020 (154)
51	gnomAD - Genomes	NC_000007.14 - 86953728	Apr 26, 2021 (155)
52	Genome of the Netherlands Release 5	NC_000007.13 - 86583044	Apr 26, 2020 (154)
53	KOREAN population from KRGDB	NC_000007.13 - 86583044	Apr 26, 2020 (154)
54	Northern Sweden	NC_000007.13 - 86583044	Jul 13, 2019 (153)
55	Qatari	NC_000007.13 - 86583044	Apr 26, 2020 (154)
56	SGDP_PRJ	NC_000007.13 - 86583044	Apr 26, 2020 (154)
57	Siberian	NC_000007.13 - 86583044	Apr 26, 2020 (154)
58	14KJPN	NC_000007.14 - 86953728	Oct 13, 2022 (156)
59	TopMed	NC_000007.14 - 86953728	Apr 26, 2021 (155)
60	UK 10K study - Twins	NC_000007.13 - 86583044	Oct 12, 2018 (152)
61	ALFA	NC_000007.14 - 86953728	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35078022	NC_000007.11:86227694:A:T	NC_000007.14:86953727:A:T	(self)
ss114047589, ss116179384, ss164766487, ss1594078884	NC_000007.12:86420979:A:T	NC_000007.14:86953727:A:T	(self)
38000644, 21145670, 15062767, 8457442, 9442212, 22245510, 8116070, 9807869, 19825483, 5302681, 21145670, ss223185791, ss234062483, ss241000951, ss560132249, ss984502877, ss1074768617, ss1325999242, ss1582292503, ss1618622295, ss1661616328, ss1927765939, ss2024565488, ss2152786327, ss2708490813, ss2855771680, ss3001571439, ss3347715663, ss3669324519, ss3734831205, ss3766824031, ss3830684036, ss3838839570, ss3867808503, ss3915068116, ss5374957448, ss5509035002, ss5643421028, ss5823142776, ss5972597266	NC_000007.13:86583043:A:T	NC_000007.14:86953727:A:T	(self)
49883861, 268093774, 58700946, 590877473, 11912136820, ss2295500452, ss3026076292, ss3720139469, ss3809997025, ss3844294325, ss4753499914, ss5273733992, ss5470734794, ss5562357926, ss5724863842, ss5859748318	NC_000007.14:86953727:A:T	NC_000007.14:86953727:A: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 rs28362761

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

rs28362761