Name: rs1490719123
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.

rs1490719123

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:99144032-99144038 (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: dupT
Variation Type: Indel Insertion and Deletion
Frequency: dupT=0.000015 (4/264690, TOPMED)
dupT=0.000022 (3/138590, GnomAD)
dupT=0.00007 (1/14050, ALFA) (+ 1 more)
dupT=0.0003 (2/6404, 1000G_30x)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TSGA10 : Intron Variant
C2orf15 : 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	14050	TTTTTTT=0.99993	TTTTTTTT=0.00007	0.999858	0.000142	0
European	Sub	9690	TTTTTTT=1.0000	TTTTTTTT=0.0000	1.0	0.0	N/A
African	Sub	2898	TTTTTTT=0.9997	TTTTTTTT=0.0003	0.99931	0.00069	0
African Others	Sub	114	TTTTTTT=1.000	TTTTTTTT=0.000	1.0	0.0	N/A
African American	Sub	2784	TTTTTTT=0.9996	TTTTTTTT=0.0004	0.999282	0.000718	0
Asian	Sub	112	TTTTTTT=1.000	TTTTTTTT=0.000	1.0	0.0	N/A
East Asian	Sub	86	TTTTTTT=1.00	TTTTTTTT=0.00	1.0	0.0	N/A
Other Asian	Sub	26	TTTTTTT=1.00	TTTTTTTT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	TTTTTTT=1.000	TTTTTTTT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TTTTTTT=1.000	TTTTTTTT=0.000	1.0	0.0	N/A
South Asian	Sub	98	TTTTTTT=1.00	TTTTTTTT=0.00	1.0	0.0	N/A
Other	Sub	496	TTTTTTT=1.000	TTTTTTTT=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	- No frequency provided	dupT=0.000015
gnomAD - Genomes	Global	Study-wide	138590	- No frequency provided	dupT=0.000022
gnomAD - Genomes	European	Sub	74928	- No frequency provided	dupT=0.00000
gnomAD - Genomes	African	Sub	41606	- No frequency provided	dupT=0.00007
gnomAD - Genomes	American	Sub	13528	- No frequency provided	dupT=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	- No frequency provided	dupT=0.0000
gnomAD - Genomes	East Asian	Sub	3102	- No frequency provided	dupT=0.0000
gnomAD - Genomes	Other	Sub	2118	- No frequency provided	dupT=0.0000
Allele Frequency Aggregator	Total	Global	14050	(T)₇=0.99993	dupT=0.00007
Allele Frequency Aggregator	European	Sub	9690	(T)₇=1.0000	dupT=0.0000
Allele Frequency Aggregator	African	Sub	2898	(T)₇=0.9997	dupT=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	610	(T)₇=1.000	dupT=0.000
Allele Frequency Aggregator	Other	Sub	496	(T)₇=1.000	dupT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(T)₇=1.000	dupT=0.000
Allele Frequency Aggregator	Asian	Sub	112	(T)₇=1.000	dupT=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(T)₇=1.00	dupT=0.00
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupT=0.0003
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupT=0.0011
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupT=0.0000
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupT=0.0000
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupT=0.0000
1000Genomes_30x	American	Sub	980	- No frequency provided	dupT=0.000

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 2	NC_000002.12:g.99144038dup
GRCh37.p13 chr 2	NC_000002.11:g.99760501dup

Gene: C2orf15, chromosome 2 open reading frame 15 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C2orf15 transcript variant 1	NM_001317992.2:c.-265+163… NM_001317992.2:c.-265+1637dup	N/A	Intron Variant
C2orf15 transcript variant 2	NM_144706.4:c.-169+1637dup	N/A	Intron Variant

Gene: TSGA10, testis specific 10 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TSGA10 transcript variant 4	NM_001349013.2:c.-519+106… NM_001349013.2:c.-519+10661dup	N/A	Intron Variant
TSGA10 transcript variant 1	NM_025244.4:c.-621+10661d… NM_025244.4:c.-621+10661dup	N/A	Intron Variant
TSGA10 transcript variant 3	NM_001349012.1:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant 5	NM_001349014.1:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant 2	NM_182911.4:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant 6	NR_146001.2:n.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant 7	NR_146053.2:n.	N/A	Genic Downstream Transcript Variant
TSGA10 transcript variant 8	NR_146054.1:n.	N/A	Genic Downstream Transcript Variant
TSGA10 transcript variant 9	NR_146055.2:n.	N/A	Genic Downstream Transcript Variant
TSGA10 transcript variant X11	XM_017005041.3:c.-529+106… XM_017005041.3:c.-529+10661dup	N/A	Intron Variant
TSGA10 transcript variant X3	XM_047445928.1:c.33+10259… XM_047445928.1:c.33+10259dup	N/A	Intron Variant
TSGA10 transcript variant X4	XM_047445929.1:c.33+10259… XM_047445929.1:c.33+10259dup	N/A	Intron Variant
TSGA10 transcript variant X5	XM_047445930.1:c.33+10259… XM_047445930.1:c.33+10259dup	N/A	Intron Variant
TSGA10 transcript variant X6	XM_047445931.1:c.33+10259… XM_047445931.1:c.33+10259dup	N/A	Intron Variant
TSGA10 transcript variant X7	XM_047445932.1:c.33+10259… XM_047445932.1:c.33+10259dup	N/A	Intron Variant
TSGA10 transcript variant X16	XM_047445934.1:c.-400+108… XM_047445934.1:c.-400+10805dup	N/A	Intron Variant
TSGA10 transcript variant X10	XM_005264023.2:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X15	XM_006712781.3:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X1	XM_011511934.1:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X8	XM_011511935.4:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X2	XM_017005035.2:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X9	XM_017005037.1:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X13	XM_017005044.2:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X17	XM_017005046.2:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X14	XM_024453158.2:c.	N/A	Genic Upstream Transcript Variant
TSGA10 transcript variant X12	XM_047445933.1: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	(T)₇=	dupT
GRCh38.p14 chr 2	NC_000002.12:g.99144032_99144038=	NC_000002.12:g.99144038dup
GRCh37.p13 chr 2	NC_000002.11:g.99760495_99760501=	NC_000002.11:g.99760501dup
C2orf15 transcript variant 1	NM_001317992.2:c.-265+1631=	NM_001317992.2:c.-265+1637dup
TSGA10 transcript variant 4	NM_001349013.2:c.-519+10661=	NM_001349013.2:c.-519+10661dup
TSGA10 transcript variant 1	NM_025244.2:c.-621+10661=	NM_025244.2:c.-621+10661dup
TSGA10 transcript variant 1	NM_025244.4:c.-621+10661=	NM_025244.4:c.-621+10661dup
C2orf15 transcript	NM_144706.2:c.-67+1631=	NM_144706.2:c.-67+1637dup
C2orf15 transcript variant 2	NM_144706.4:c.-169+1631=	NM_144706.4:c.-169+1637dup
TSGA10 transcript variant X11	XM_017005041.3:c.-529+10661=	XM_017005041.3:c.-529+10661dup
TSGA10 transcript variant X3	XM_047445928.1:c.33+10259=	XM_047445928.1:c.33+10259dup
TSGA10 transcript variant X4	XM_047445929.1:c.33+10259=	XM_047445929.1:c.33+10259dup
TSGA10 transcript variant X5	XM_047445930.1:c.33+10259=	XM_047445930.1:c.33+10259dup
TSGA10 transcript variant X6	XM_047445931.1:c.33+10259=	XM_047445931.1:c.33+10259dup
TSGA10 transcript variant X7	XM_047445932.1:c.33+10259=	XM_047445932.1:c.33+10259dup
TSGA10 transcript variant X16	XM_047445934.1:c.-400+10805=	XM_047445934.1:c.-400+10805dup

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#.

5 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4046888603	Apr 27, 2021 (155)
2	TOPMED	ss4516224539	Apr 27, 2021 (155)
3	1000G_HIGH_COVERAGE	ss5249211501	Oct 12, 2022 (156)
4	1000G_HIGH_COVERAGE	ss5525065318	Oct 12, 2022 (156)
5	SANFORD_IMAGENETICS	ss5629345460	Oct 12, 2022 (156)
6	1000Genomes_30x	NC_000002.12 - 99144032	Oct 12, 2022 (156)
7	gnomAD - Genomes	NC_000002.12 - 99144032	Apr 27, 2021 (155)
8	TopMed	NC_000002.12 - 99144032	Apr 27, 2021 (155)
9	ALFA	NC_000002.12 - 99144032	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
ss5629345460	NC_000002.11:99760494::T	NC_000002.12:99144031:TTTTTTT:TTTT… NC_000002.12:99144031:TTTTTTT:TTTTTTTT
12591253, 67255207, 320047418, ss4046888603, ss4516224539, ss5249211501, ss5525065318	NC_000002.12:99144031::T	NC_000002.12:99144031:TTTTTTT:TTTT… NC_000002.12:99144031:TTTTTTT:TTTTTTTT	(self)
6699323123	NC_000002.12:99144031:TTTTTTT:TTTT… NC_000002.12:99144031:TTTTTTT:TTTTTTTT	NC_000002.12:99144031:TTTTTTT:TTTT… NC_000002.12:99144031:TTTTTTT:TTTTTTTT	(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 rs1490719123

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

rs1490719123