Name: rs1198012015
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.

rs1198012015

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:43650311-43650320 (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: delT / dupT / dupTT
Variation Type: Indel Insertion and Deletion
Frequency: delT=0.010745 (2844/264690, TOPMED)
dupT=0.00036 (6/16760, 8.3KJPN)
dupT=0.00044 (7/15888, ALFA) (+ 2 more)
dupT=0.0104 (19/1832, Korea1K)
dupT=0.003 (2/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PLAUR : 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	HTRZ	HWEP
Total	Global	15888	TTTTTTTTTT=0.99956	TTTTTTTTT=0.00000, TTTTTTTTTTT=0.00044, TTTTTTTTTTTT=0.00000	0.999119	0.000881	0
European	Sub	12028	TTTTTTTTTT=0.99942	TTTTTTTTT=0.00000, TTTTTTTTTTT=0.00058, TTTTTTTTTTTT=0.00000	0.998836	0.001164	0
African	Sub	2452	TTTTTTTTTT=1.0000	TTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000	1.0	0.0	N/A
African Others	Sub	82	TTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
African American	Sub	2370	TTTTTTTTTT=1.0000	TTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000	1.0	0.0	N/A
Asian	Sub	106	TTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
East Asian	Sub	82	TTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Latin American 1	Sub	144	TTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
Latin American 2	Sub	608	TTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
South Asian	Sub	94	TTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other	Sub	456	TTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	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
TopMed	Global	Study-wide	264690	(T)₁₀=0.989255	delT=0.010745
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupT=0.00036
Allele Frequency Aggregator	Total	Global	15888	(T)₁₀=0.99956	delT=0.00000, dupT=0.00044, dupTT=0.00000
Allele Frequency Aggregator	European	Sub	12028	(T)₁₀=0.99942	delT=0.00000, dupT=0.00058, dupTT=0.00000
Allele Frequency Aggregator	African	Sub	2452	(T)₁₀=1.0000	delT=0.0000, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	608	(T)₁₀=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	456	(T)₁₀=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	144	(T)₁₀=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Asian	Sub	106	(T)₁₀=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(T)₁₀=1.00	delT=0.00, dupT=0.00, dupTT=0.00
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupT=0.0104
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupT=0.003

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 19	NC_000019.10:g.43650320del
GRCh38.p14 chr 19	NC_000019.10:g.43650320dup
GRCh38.p14 chr 19	NC_000019.10:g.43650319_43650320dup
GRCh37.p13 chr 19	NC_000019.9:g.44154472del
GRCh37.p13 chr 19	NC_000019.9:g.44154472dup
GRCh37.p13 chr 19	NC_000019.9:g.44154471_44154472dup
PLAUR RefSeqGene (LRG_637)	NG_032898.1:g.25036del
PLAUR RefSeqGene (LRG_637)	NG_032898.1:g.25036dup
PLAUR RefSeqGene (LRG_637)	NG_032898.1:g.25035_25036dup

Gene: PLAUR, plasminogen activator, urokinase receptor (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLAUR transcript variant 2	NM_001005376.3:c.754+1914… NM_001005376.3:c.754+1914del	N/A	Intron Variant
PLAUR transcript variant 3	NM_001005377.3:c.620-1168… NM_001005377.3:c.620-1168del	N/A	Intron Variant
PLAUR transcript variant 4	NM_001301037.2:c.608-1168… NM_001301037.2:c.608-1168del	N/A	Intron Variant
PLAUR transcript variant 1	NM_002659.4:c.755-1168del	N/A	Intron Variant
PLAUR transcript variant X2	XM_017026872.3:c.740-1168… XM_017026872.3:c.740-1168del	N/A	Intron Variant
PLAUR transcript variant X1	XM_047438925.1:c.755-1168… XM_047438925.1:c.755-1168del	N/A	Intron Variant
PLAUR transcript variant X3	XM_047438926.1:c.620-1168… XM_047438926.1:c.620-1168del	N/A	Intron Variant
PLAUR transcript variant X4	XM_047438927.1:c.611-1168… XM_047438927.1:c.611-1168del	N/A	Intron Variant
PLAUR transcript variant X5	XM_047438928.1:c.608-1168… XM_047438928.1:c.608-1168del	N/A	Intron Variant
PLAUR transcript variant X6	XM_047438929.1:c.605-1168… XM_047438929.1:c.605-1168del	N/A	Intron Variant
PLAUR transcript variant X7	XM_047438930.1:c.593-1168… XM_047438930.1:c.593-1168del	N/A	Intron Variant
PLAUR transcript variant X8	XM_047438931.1:c.739+1914… XM_047438931.1:c.739+1914del	N/A	Intron Variant
PLAUR transcript variant X10	XM_047438933.1:c.476-1168… XM_047438933.1:c.476-1168del	N/A	Intron Variant
PLAUR transcript variant X11	XM_047438934.1:c.473-1168… XM_047438934.1:c.473-1168del	N/A	Intron Variant
PLAUR transcript variant X12	XM_047438935.1:c.619+1914… XM_047438935.1:c.619+1914del	N/A	Intron Variant
PLAUR transcript variant X13	XM_047438936.1:c.610+1914… XM_047438936.1:c.610+1914del	N/A	Intron Variant
PLAUR transcript variant X14	XM_047438937.1:c.475+1914… XM_047438937.1:c.475+1914del	N/A	Intron Variant
PLAUR transcript variant X9	XM_047438932.1:c.	N/A	Genic Downstream 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	(T)₁₀=	delT	dupT	dupTT
GRCh38.p14 chr 19	NC_000019.10:g.43650311_43650320=	NC_000019.10:g.43650320del	NC_000019.10:g.43650320dup	NC_000019.10:g.43650319_43650320dup
GRCh37.p13 chr 19	NC_000019.9:g.44154463_44154472=	NC_000019.9:g.44154472del	NC_000019.9:g.44154472dup	NC_000019.9:g.44154471_44154472dup
PLAUR RefSeqGene (LRG_637)	NG_032898.1:g.25027_25036=	NG_032898.1:g.25036del	NG_032898.1:g.25036dup	NG_032898.1:g.25035_25036dup
PLAUR transcript variant 2	NM_001005376.2:c.754+1914=	NM_001005376.2:c.754+1914del	NM_001005376.2:c.754+1914dup	NM_001005376.2:c.754+1913_754+1914dup
PLAUR transcript variant 2	NM_001005376.3:c.754+1914=	NM_001005376.3:c.754+1914del	NM_001005376.3:c.754+1914dup	NM_001005376.3:c.754+1913_754+1914dup
PLAUR transcript variant 3	NM_001005377.2:c.620-1168=	NM_001005377.2:c.620-1168del	NM_001005377.2:c.620-1168dup	NM_001005377.2:c.620-1169_620-1168dup
PLAUR transcript variant 3	NM_001005377.3:c.620-1168=	NM_001005377.3:c.620-1168del	NM_001005377.3:c.620-1168dup	NM_001005377.3:c.620-1169_620-1168dup
PLAUR transcript variant 4	NM_001301037.2:c.608-1168=	NM_001301037.2:c.608-1168del	NM_001301037.2:c.608-1168dup	NM_001301037.2:c.608-1169_608-1168dup
PLAUR transcript variant 1	NM_002659.3:c.755-1168=	NM_002659.3:c.755-1168del	NM_002659.3:c.755-1168dup	NM_002659.3:c.755-1169_755-1168dup
PLAUR transcript variant 1	NM_002659.4:c.755-1168=	NM_002659.4:c.755-1168del	NM_002659.4:c.755-1168dup	NM_002659.4:c.755-1169_755-1168dup
PLAUR transcript variant X1	XM_005258988.1:c.740-1168=	XM_005258988.1:c.740-1168del	XM_005258988.1:c.740-1168dup	XM_005258988.1:c.740-1169_740-1168dup
PLAUR transcript variant X2	XM_005258989.1:c.608-1168=	XM_005258989.1:c.608-1168del	XM_005258989.1:c.608-1168dup	XM_005258989.1:c.608-1169_608-1168dup
PLAUR transcript variant X2	XM_017026872.3:c.740-1168=	XM_017026872.3:c.740-1168del	XM_017026872.3:c.740-1168dup	XM_017026872.3:c.740-1169_740-1168dup
PLAUR transcript variant X1	XM_047438925.1:c.755-1168=	XM_047438925.1:c.755-1168del	XM_047438925.1:c.755-1168dup	XM_047438925.1:c.755-1169_755-1168dup
PLAUR transcript variant X3	XM_047438926.1:c.620-1168=	XM_047438926.1:c.620-1168del	XM_047438926.1:c.620-1168dup	XM_047438926.1:c.620-1169_620-1168dup
PLAUR transcript variant X4	XM_047438927.1:c.611-1168=	XM_047438927.1:c.611-1168del	XM_047438927.1:c.611-1168dup	XM_047438927.1:c.611-1169_611-1168dup
PLAUR transcript variant X5	XM_047438928.1:c.608-1168=	XM_047438928.1:c.608-1168del	XM_047438928.1:c.608-1168dup	XM_047438928.1:c.608-1169_608-1168dup
PLAUR transcript variant X6	XM_047438929.1:c.605-1168=	XM_047438929.1:c.605-1168del	XM_047438929.1:c.605-1168dup	XM_047438929.1:c.605-1169_605-1168dup
PLAUR transcript variant X7	XM_047438930.1:c.593-1168=	XM_047438930.1:c.593-1168del	XM_047438930.1:c.593-1168dup	XM_047438930.1:c.593-1169_593-1168dup
PLAUR transcript variant X8	XM_047438931.1:c.739+1914=	XM_047438931.1:c.739+1914del	XM_047438931.1:c.739+1914dup	XM_047438931.1:c.739+1913_739+1914dup
PLAUR transcript variant X10	XM_047438933.1:c.476-1168=	XM_047438933.1:c.476-1168del	XM_047438933.1:c.476-1168dup	XM_047438933.1:c.476-1169_476-1168dup
PLAUR transcript variant X11	XM_047438934.1:c.473-1168=	XM_047438934.1:c.473-1168del	XM_047438934.1:c.473-1168dup	XM_047438934.1:c.473-1169_473-1168dup
PLAUR transcript variant X12	XM_047438935.1:c.619+1914=	XM_047438935.1:c.619+1914del	XM_047438935.1:c.619+1914dup	XM_047438935.1:c.619+1913_619+1914dup
PLAUR transcript variant X13	XM_047438936.1:c.610+1914=	XM_047438936.1:c.610+1914del	XM_047438936.1:c.610+1914dup	XM_047438936.1:c.610+1913_610+1914dup
PLAUR transcript variant X14	XM_047438937.1:c.475+1914=	XM_047438937.1:c.475+1914del	XM_047438937.1:c.475+1914dup	XM_047438937.1:c.475+1913_475+1914dup

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#.

15 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SWEGEN	ss3017524592	Jan 10, 2018 (151)
2	EVA_DECODE	ss3702826522	Jul 13, 2019 (153)
3	EVA_DECODE	ss3702826523	Jul 13, 2019 (153)
4	ACPOP	ss3743063915	Jul 13, 2019 (153)
5	KOGIC	ss3981416135	Apr 27, 2020 (154)
6	GNOMAD	ss4331790349	Apr 26, 2021 (155)
7	GNOMAD	ss4331790350	Apr 26, 2021 (155)
8	TOPMED	ss5075867061	Apr 26, 2021 (155)
9	TOMMO_GENOMICS	ss5227907677	Apr 26, 2021 (155)
10	1000G_HIGH_COVERAGE	ss5307361728	Oct 16, 2022 (156)
11	HUGCELL_USP	ss5499862004	Oct 16, 2022 (156)
12	HUGCELL_USP	ss5499862005	Oct 16, 2022 (156)
13	TOMMO_GENOMICS	ss5786588498	Oct 16, 2022 (156)
14	TOMMO_GENOMICS	ss5786588499	Oct 16, 2022 (156)
15	YY_MCH	ss5817628429	Oct 16, 2022 (156)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 540937341 (NC_000019.10:43650310::T 1384/132908) Row 540937342 (NC_000019.10:43650310::TT 1/132966) Row 540937344 (NC_000019.10:43650310:T: 1411/132954)	-	Apr 26, 2021 (155)
17	gnomAD - Genomes Submission ignored due to conflicting rows: Row 540937341 (NC_000019.10:43650310::T 1384/132908) Row 540937342 (NC_000019.10:43650310::TT 1/132966) Row 540937344 (NC_000019.10:43650310:T: 1411/132954)	-	Apr 26, 2021 (155)
18	gnomAD - Genomes Submission ignored due to conflicting rows: Row 540937341 (NC_000019.10:43650310::T 1384/132908) Row 540937342 (NC_000019.10:43650310::TT 1/132966) Row 540937344 (NC_000019.10:43650310:T: 1411/132954)	-	Apr 26, 2021 (155)
19	Korean Genome Project	NC_000019.10 - 43650311	Apr 27, 2020 (154)
20	Northern Sweden	NC_000019.9 - 44154463	Jul 13, 2019 (153)
21	8.3KJPN	NC_000019.9 - 44154463	Apr 26, 2021 (155)
22	14KJPN Submission ignored due to conflicting rows: Row 120425602 (NC_000019.10:43650310:T: 10/28250) Row 120425603 (NC_000019.10:43650310::T 10/28250)	-	Oct 16, 2022 (156)
23	14KJPN Submission ignored due to conflicting rows: Row 120425602 (NC_000019.10:43650310:T: 10/28250) Row 120425603 (NC_000019.10:43650310::T 10/28250)	-	Oct 16, 2022 (156)
24	TopMed	NC_000019.10 - 43650311	Apr 26, 2021 (155)
25	ALFA	NC_000019.10 - 43650311	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
291412725, ss3702826522, ss5075867061, ss5307361728, ss5499862004, ss5786588498	NC_000019.10:43650310:T:	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTT	(self)
8959644285	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTT	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTT	(self)
16348780, 85876984, ss3017524592, ss3743063915, ss5227907677	NC_000019.9:44154462::T	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTT	(self)
37794136, ss3981416135, ss4331790349, ss5499862005, ss5786588499, ss5817628429	NC_000019.10:43650310::T	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTT	(self)
8959644285	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTT	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTT	(self)
ss3702826523	NC_000019.10:43650311::T	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTT	(self)
ss4331790350	NC_000019.10:43650310::TT	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTTT	(self)
8959644285	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTTT	NC_000019.10:43650310:TTTTTTTTTT:T… NC_000019.10:43650310:TTTTTTTTTT:TTTTTTTTTTTT	(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 rs1198012015

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

rs1198012015