Name: rs3078519
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.

rs3078519

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:132688826-132688828 (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: delTG / dupTG
Variation Type: Indel Insertion and Deletion
Frequency: GTG=0.00007 (2/28258, 14KJPN)
GTG=0.00018 (3/16760, 8.3KJPN)
GTG=0.0092 (46/5008, 1000G) (+ 6 more)
GTG=0.0033 (15/4478, Estonian)
GTG=0.0034 (15/4468, ALFA)
GTG=0.0000 (0/1832, Korea1K)
GTG=0.014 (14/998, GoNL)
GTG=0.002 (1/600, NorthernSweden)
GTG=0.000 (0/212, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: INPP5A : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	4468	GTG=0.0034	G=0.0000, GTGTG=0.9966	0.0	0.993286	0.006714	0
European	Sub	4460	GTG=0.0034	G=0.0000, GTGTG=0.9966	0.0	0.993274	0.006726	0
African	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
African Others	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
African American	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
Asian	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
East Asian	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
Other Asian	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
Latin American 1	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
Latin American 2	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
South Asian	Sub	0	GTG=0	G=0, GTGTG=0	0	0	0	N/A
Other	Sub	8	GTG=0.0	G=0.0, GTGTG=1.0	0.0	1.0	0.0	N/A

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
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupTG=0.99993
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupTG=0.99982
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupTG=0.9908
1000Genomes	African	Sub	1322	- No frequency provided	dupTG=1.0000
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupTG=0.9940
1000Genomes	Europe	Sub	1006	- No frequency provided	dupTG=0.9831
1000Genomes	South Asian	Sub	978	- No frequency provided	dupTG=0.987
1000Genomes	American	Sub	694	- No frequency provided	dupTG=0.986
Genetic variation in the Estonian population	Estonian	Study-wide	4478	- No frequency provided	dupTG=0.9967
Allele Frequency Aggregator	Total	Global	4468	GTG=0.0034	delTG=0.0000, dupTG=0.9966
Allele Frequency Aggregator	European	Sub	4460	GTG=0.0034	delTG=0.0000, dupTG=0.9966
Allele Frequency Aggregator	Other	Sub	8	GTG=0.0	delTG=0.0, dupTG=1.0
Allele Frequency Aggregator	Latin American 1	Sub	0	GTG=0	delTG=0, dupTG=0
Allele Frequency Aggregator	Latin American 2	Sub	0	GTG=0	delTG=0, dupTG=0
Allele Frequency Aggregator	South Asian	Sub	0	GTG=0	delTG=0, dupTG=0
Allele Frequency Aggregator	African	Sub	0	GTG=0	delTG=0, dupTG=0
Allele Frequency Aggregator	Asian	Sub	0	GTG=0	delTG=0, dupTG=0
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupTG=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupTG=0.986
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupTG=0.998
A Vietnamese Genetic Variation Database	Global	Study-wide	212	- No frequency provided	dupTG=1.000

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 10	NC_000010.11:g.132688827_132688828del
GRCh38.p14 chr 10	NC_000010.11:g.132688827_132688828dup
GRCh37.p13 chr 10	NC_000010.10:g.134502331_134502332del
GRCh37.p13 chr 10	NC_000010.10:g.134502331_134502332dup

Gene: INPP5A, inositol polyphosphate-5-phosphatase A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
INPP5A transcript variant 2	NM_001321042.2:c.115-1565… NM_001321042.2:c.115-1565_115-1564del	N/A	Intron Variant
INPP5A transcript variant 1	NM_005539.5:c.307-1565_30… NM_005539.5:c.307-1565_307-1564del	N/A	Intron Variant
INPP5A transcript variant X1	XM_017016204.2:c.133-1565… XM_017016204.2:c.133-1565_133-1564del	N/A	Intron Variant
INPP5A transcript variant X3	XM_017016205.2:c.307-1565… XM_017016205.2:c.307-1565_307-1564del	N/A	Intron Variant
INPP5A transcript variant X5	XR_001747104.2:n.	N/A	Intron Variant
INPP5A transcript variant X2	XR_007061962.1:n.	N/A	Intron Variant
INPP5A transcript variant X6	XR_007061963.1:n.	N/A	Intron Variant
INPP5A transcript variant X4	XR_945735.2: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	GTG=	delTG	dupTG
GRCh38.p14 chr 10	NC_000010.11:g.132688826_132688828=	NC_000010.11:g.132688827_132688828del	NC_000010.11:g.132688827_132688828dup
GRCh37.p13 chr 10	NC_000010.10:g.134502330_134502332=	NC_000010.10:g.134502331_134502332del	NC_000010.10:g.134502331_134502332dup
INPP5A transcript variant 2	NM_001321042.2:c.115-1566=	NM_001321042.2:c.115-1565_115-1564del	NM_001321042.2:c.115-1565_115-1564dup
INPP5A transcript	NM_005539.3:c.307-1566=	NM_005539.3:c.307-1565_307-1564del	NM_005539.3:c.307-1565_307-1564dup
INPP5A transcript variant 1	NM_005539.5:c.307-1566=	NM_005539.5:c.307-1565_307-1564del	NM_005539.5:c.307-1565_307-1564dup
INPP5A transcript variant X1	XM_005252681.1:c.307-1566=	XM_005252681.1:c.307-1565_307-1564del	XM_005252681.1:c.307-1565_307-1564dup
INPP5A transcript variant X1	XM_017016204.2:c.133-1566=	XM_017016204.2:c.133-1565_133-1564del	XM_017016204.2:c.133-1565_133-1564dup
INPP5A transcript variant X3	XM_017016205.2:c.307-1566=	XM_017016205.2:c.307-1565_307-1564del	XM_017016205.2:c.307-1565_307-1564dup

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#.

50 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4309950	Dec 03, 2013 (138)
2	HGSV	ss81722951	Dec 04, 2013 (138)
3	HGSV	ss83189278	Dec 05, 2013 (138)
4	BL	ss256145714	May 09, 2011 (135)
5	GMI	ss287868555	May 09, 2011 (134)
6	GMI	ss289047316	May 04, 2012 (137)
7	1000GENOMES	ss327298694	May 09, 2011 (135)
8	1000GENOMES	ss327382365	May 09, 2011 (135)
9	LUNTER	ss552088257	Apr 25, 2013 (138)
10	TISHKOFF	ss561497378	Apr 25, 2013 (138)
11	SSMP	ss663965458	Apr 01, 2015 (144)
12	BILGI_BIOE	ss666521502	Apr 25, 2013 (138)
13	EVA-GONL	ss988101512	Aug 21, 2014 (142)
14	1000GENOMES	ss1370347182	Aug 21, 2014 (142)
15	DDI	ss1536675299	Apr 01, 2015 (144)
16	EVA_DECODE	ss1597781510	Apr 01, 2015 (144)
17	HAMMER_LAB	ss1806647790	Sep 08, 2015 (146)
18	GENOMED	ss1967267860	Jul 19, 2016 (147)
19	JJLAB	ss2031053492	Sep 14, 2016 (149)
20	SYSTEMSBIOZJU	ss2627705117	Nov 08, 2017 (151)
21	SWEGEN	ss3007419580	Nov 08, 2017 (151)
22	MCHAISSO	ss3063676231	Nov 08, 2017 (151)
23	MCHAISSO	ss3064499115	Nov 08, 2017 (151)
24	MCHAISSO	ss3065410990	Nov 08, 2017 (151)
25	BEROUKHIMLAB	ss3644311254	Oct 12, 2018 (152)
26	BIOINF_KMB_FNS_UNIBA	ss3645172857	Oct 12, 2018 (152)
27	URBANLAB	ss3649506497	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3674839950	Jul 13, 2019 (153)
29	EVA_DECODE	ss3691019942	Jul 13, 2019 (153)
30	ACPOP	ss3737829060	Jul 13, 2019 (153)
31	PACBIO	ss3786834839	Jul 13, 2019 (153)
32	PACBIO	ss3791991214	Jul 13, 2019 (153)
33	PACBIO	ss3796873405	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3814171722	Jul 13, 2019 (153)
35	EVA	ss3832422931	Apr 26, 2020 (154)
36	EVA	ss3839753815	Apr 26, 2020 (154)
37	EVA	ss3845229844	Apr 26, 2020 (154)
38	KOGIC	ss3969011792	Apr 26, 2020 (154)
39	GNOMAD	ss4228473022	Apr 26, 2021 (155)
40	GNOMAD	ss4228473024	Apr 26, 2021 (155)
41	TOMMO_GENOMICS	ss5200219724	Apr 26, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5286053811	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5481417046	Oct 16, 2022 (156)
44	SANFORD_IMAGENETICS	ss5650431745	Oct 16, 2022 (156)
45	TOMMO_GENOMICS	ss5746825232	Oct 16, 2022 (156)
46	YY_MCH	ss5812035784	Oct 16, 2022 (156)
47	EVA	ss5825193713	Oct 16, 2022 (156)
48	EVA	ss5849817913	Oct 16, 2022 (156)
49	EVA	ss5881211597	Oct 16, 2022 (156)
50	EVA	ss5980650664	Oct 16, 2022 (156)
51	1000Genomes	NC_000010.10 - 134502330	Oct 12, 2018 (152)
52	Genetic variation in the Estonian population	NC_000010.10 - 134502330	Oct 12, 2018 (152)
53	gnomAD - Genomes Submission ignored due to conflicting rows: Row 368646987 (NC_000010.11:132688825::GT 138722/140094) Row 368646989 (NC_000010.11:132688825:GT: 1/140094)	-	Apr 26, 2021 (155)
54	gnomAD - Genomes Submission ignored due to conflicting rows: Row 368646987 (NC_000010.11:132688825::GT 138722/140094) Row 368646989 (NC_000010.11:132688825:GT: 1/140094)	-	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000010.10 - 134502330	Apr 26, 2020 (154)
56	Korean Genome Project	NC_000010.11 - 132688826	Apr 26, 2020 (154)
57	Northern Sweden	NC_000010.10 - 134502330	Jul 13, 2019 (153)
58	8.3KJPN	NC_000010.10 - 134502330	Apr 26, 2021 (155)
59	14KJPN	NC_000010.11 - 132688826	Oct 16, 2022 (156)
60	A Vietnamese Genetic Variation Database	NC_000010.10 - 134502330	Jul 13, 2019 (153)
61	ALFA	NC_000010.11 - 132688826	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)
rs59256771	May 24, 2008 (130)
rs68151156	May 15, 2013 (138)
rs68151157	Feb 27, 2009 (130)
rs68151158	Feb 27, 2009 (130)
rs68151159	Feb 27, 2009 (130)
rs68151160	Feb 27, 2009 (130)
rs139931535	Sep 17, 2011 (135)
rs971624664	Nov 08, 2017 (151)
rs150167940	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4228473024	NC_000010.11:132688825:GT:	NC_000010.11:132688825:GTG:G	(self)
12115554830	NC_000010.11:132688825:GTG:G	NC_000010.11:132688825:GTG:G	(self)
ss256145714, ss289047316, ss327298694, ss327382365, ss552088257, ss1597781510	NC_000010.9:134352319::GT	NC_000010.11:132688825:GTG:GTGTG	(self)
52197761, 20578198, 12928525, 11113925, 58189031, 6438361, ss663965458, ss666521502, ss988101512, ss1370347182, ss1536675299, ss1806647790, ss1967267860, ss2031053492, ss2627705117, ss3007419580, ss3644311254, ss3674839950, ss3737829060, ss3786834839, ss3791991214, ss3796873405, ss3832422931, ss3839753815, ss5200219724, ss5650431745, ss5825193713, ss5980650664	NC_000010.10:134502329::GT	NC_000010.11:132688825:GTG:GTGTG	(self)
ss561497378	NC_000010.10:134502332::TG	NC_000010.11:132688825:GTG:GTGTG	(self)
25389793, 80662336, ss3063676231, ss3064499115, ss3065410990, ss3645172857, ss3649506497, ss3691019942, ss3814171722, ss3845229844, ss3969011792, ss4228473022, ss5286053811, ss5481417046, ss5746825232, ss5812035784, ss5849817913, ss5881211597	NC_000010.11:132688825::GT	NC_000010.11:132688825:GTG:GTGTG	(self)
12115554830	NC_000010.11:132688825:GTG:GTGTG	NC_000010.11:132688825:GTG:GTGTG	(self)
ss287868555	NT_008818.16:5736260::GT	NC_000010.11:132688825:GTG:GTGTG	(self)
ss4309950, ss81722951, ss83189278	NT_008818.16:5736263::TG	NC_000010.11:132688825:GTG:GTGTG	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2342564585	NC_000010.10:134502329:GT:	NC_000010.11:132688825:GTG:G

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs3078519

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

rs3078519