Name: rs1489390916
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.

rs1489390916

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:99141044 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000004 (1/264690, TOPMED)
A=0.00000 (0/10680, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TSGA10 : Intron Variant
C2orf15 : 2KB Upstream 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	HWEP
Total	Global	10680	C=1.00000	A=0.00000	1.0	N/A
European	Sub	6962	C=1.0000	A=0.0000	1.0	N/A
African	Sub	2294	C=1.0000	A=0.0000	1.0	N/A
African Others	Sub	84	C=1.00	A=0.00	1.0	N/A
African American	Sub	2210	C=1.0000	A=0.0000	1.0	N/A
Asian	Sub	108	C=1.000	A=0.000	1.0	N/A
East Asian	Sub	84	C=1.00	A=0.00	1.0	N/A
Other Asian	Sub	24	C=1.00	A=0.00	1.0	N/A
Latin American 1	Sub	146	C=1.000	A=0.000	1.0	N/A
Latin American 2	Sub	610	C=1.000	A=0.000	1.0	N/A
South Asian	Sub	94	C=1.00	A=0.00	1.0	N/A
Other	Sub	466	C=1.000	A=0.000	1.0	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	C=0.999996	A=0.000004
Allele Frequency Aggregator	Total	Global	10680	C=1.00000	A=0.00000
Allele Frequency Aggregator	European	Sub	6962	C=1.0000	A=0.0000
Allele Frequency Aggregator	African	Sub	2294	C=1.0000	A=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	A=0.000
Allele Frequency Aggregator	Other	Sub	466	C=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	108	C=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	94	C=1.00	A=0.00

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.99141044C>A
GRCh38.p14 chr 2	NC_000002.12:g.99141044C>T
GRCh37.p13 chr 2	NC_000002.11:g.99757507C>A
GRCh37.p13 chr 2	NC_000002.11:g.99757507C>T

Gene: TSGA10, testis specific 10 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TSGA10 transcript variant 3	NM_001349012.1:c.-313+300… NM_001349012.1:c.-313+300G>T	N/A	Intron Variant
TSGA10 transcript variant 4	NM_001349013.2:c.-519+136… NM_001349013.2:c.-519+13649G>T	N/A	Intron Variant
TSGA10 transcript variant 5	NM_001349014.1:c.-492+384… NM_001349014.1:c.-492+384G>T	N/A	Intron Variant
TSGA10 transcript variant 1	NM_025244.4:c.-621+13649G… NM_025244.4:c.-621+13649G>T	N/A	Intron Variant
TSGA10 transcript variant 2	NM_182911.4:c.-485+384G>T	N/A	Intron Variant
TSGA10 transcript variant 6	NR_146001.2:n.	N/A	Intron 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 X10	XM_005264023.2:c.-529+300… XM_005264023.2:c.-529+300G>T	N/A	Intron Variant
TSGA10 transcript variant X1	XM_011511934.1:c.72+24G>T	N/A	Intron Variant
TSGA10 transcript variant X8	XM_011511935.4:c.72+24G>T	N/A	Intron Variant
TSGA10 transcript variant X2	XM_017005035.2:c.57+39G>T	N/A	Intron Variant
TSGA10 transcript variant X9	XM_017005037.1:c.72+24G>T	N/A	Intron Variant
TSGA10 transcript variant X11	XM_017005041.3:c.-529+136… XM_017005041.3:c.-529+13649G>T	N/A	Intron Variant
TSGA10 transcript variant X3	XM_047445928.1:c.33+13247… XM_047445928.1:c.33+13247G>T	N/A	Intron Variant
TSGA10 transcript variant X4	XM_047445929.1:c.33+13247… XM_047445929.1:c.33+13247G>T	N/A	Intron Variant
TSGA10 transcript variant X5	XM_047445930.1:c.33+13247… XM_047445930.1:c.33+13247G>T	N/A	Intron Variant
TSGA10 transcript variant X6	XM_047445931.1:c.33+13247… XM_047445931.1:c.33+13247G>T	N/A	Intron Variant
TSGA10 transcript variant X7	XM_047445932.1:c.33+13247… XM_047445932.1:c.33+13247G>T	N/A	Intron Variant
TSGA10 transcript variant X12	XM_047445933.1:c.-400+384… XM_047445933.1:c.-400+384G>T	N/A	Intron Variant
TSGA10 transcript variant X16	XM_047445934.1:c.-400+137… XM_047445934.1:c.-400+13793G>T	N/A	Intron Variant
TSGA10 transcript variant X15	XM_006712781.3: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

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

Molecule type	Change	Amino acid[Codon]	SO Term
C2orf15 transcript variant 1	NM_001317992.2:c.	N/A	Upstream Transcript Variant
C2orf15 transcript variant 2	NM_144706.4:c.	N/A	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	C=	A	T
GRCh38.p14 chr 2	NC_000002.12:g.99141044=	NC_000002.12:g.99141044C>A	NC_000002.12:g.99141044C>T
GRCh37.p13 chr 2	NC_000002.11:g.99757507=	NC_000002.11:g.99757507C>A	NC_000002.11:g.99757507C>T
TSGA10 transcript variant 3	NM_001349012.1:c.-313+300=	NM_001349012.1:c.-313+300G>T	NM_001349012.1:c.-313+300G>A
TSGA10 transcript variant 4	NM_001349013.2:c.-519+13649=	NM_001349013.2:c.-519+13649G>T	NM_001349013.2:c.-519+13649G>A
TSGA10 transcript variant 5	NM_001349014.1:c.-492+384=	NM_001349014.1:c.-492+384G>T	NM_001349014.1:c.-492+384G>A
TSGA10 transcript variant 1	NM_025244.2:c.-621+13649=	NM_025244.2:c.-621+13649G>T	NM_025244.2:c.-621+13649G>A
TSGA10 transcript variant 1	NM_025244.4:c.-621+13649=	NM_025244.4:c.-621+13649G>T	NM_025244.4:c.-621+13649G>A
TSGA10 transcript variant 2	NM_182911.3:c.-485+384=	NM_182911.3:c.-485+384G>T	NM_182911.3:c.-485+384G>A
TSGA10 transcript variant 2	NM_182911.4:c.-485+384=	NM_182911.4:c.-485+384G>T	NM_182911.4:c.-485+384G>A
TSGA10 transcript variant X1	XM_005264022.1:c.57+39=	XM_005264022.1:c.57+39G>T	XM_005264022.1:c.57+39G>A
TSGA10 transcript variant X7	XM_005264023.1:c.-529+300=	XM_005264023.1:c.-529+300G>T	XM_005264023.1:c.-529+300G>A
TSGA10 transcript variant X10	XM_005264023.2:c.-529+300=	XM_005264023.2:c.-529+300G>T	XM_005264023.2:c.-529+300G>A
TSGA10 transcript variant X4	XM_005264024.1:c.-690+300=	XM_005264024.1:c.-690+300G>T	XM_005264024.1:c.-690+300G>A
TSGA10 transcript variant X9	XM_005264025.1:c.-665+300=	XM_005264025.1:c.-665+300G>T	XM_005264025.1:c.-665+300G>A
TSGA10 transcript variant X19	XM_005264026.1:c.-646+300=	XM_005264026.1:c.-646+300G>T	XM_005264026.1:c.-646+300G>A
TSGA10 transcript variant X20	XM_005264027.1:c.-485+300=	XM_005264027.1:c.-485+300G>T	XM_005264027.1:c.-485+300G>A
TSGA10 transcript variant X25	XM_005264029.1:c.-485+39=	XM_005264029.1:c.-485+39G>T	XM_005264029.1:c.-485+39G>A
TSGA10 transcript variant X1	XM_011511934.1:c.72+24=	XM_011511934.1:c.72+24G>T	XM_011511934.1:c.72+24G>A
TSGA10 transcript variant X8	XM_011511935.4:c.72+24=	XM_011511935.4:c.72+24G>T	XM_011511935.4:c.72+24G>A
TSGA10 transcript variant X2	XM_017005035.2:c.57+39=	XM_017005035.2:c.57+39G>T	XM_017005035.2:c.57+39G>A
TSGA10 transcript variant X9	XM_017005037.1:c.72+24=	XM_017005037.1:c.72+24G>T	XM_017005037.1:c.72+24G>A
TSGA10 transcript variant X11	XM_017005041.3:c.-529+13649=	XM_017005041.3:c.-529+13649G>T	XM_017005041.3:c.-529+13649G>A
TSGA10 transcript variant X3	XM_047445928.1:c.33+13247=	XM_047445928.1:c.33+13247G>T	XM_047445928.1:c.33+13247G>A
TSGA10 transcript variant X4	XM_047445929.1:c.33+13247=	XM_047445929.1:c.33+13247G>T	XM_047445929.1:c.33+13247G>A
TSGA10 transcript variant X5	XM_047445930.1:c.33+13247=	XM_047445930.1:c.33+13247G>T	XM_047445930.1:c.33+13247G>A
TSGA10 transcript variant X6	XM_047445931.1:c.33+13247=	XM_047445931.1:c.33+13247G>T	XM_047445931.1:c.33+13247G>A
TSGA10 transcript variant X7	XM_047445932.1:c.33+13247=	XM_047445932.1:c.33+13247G>T	XM_047445932.1:c.33+13247G>A
TSGA10 transcript variant X12	XM_047445933.1:c.-400+384=	XM_047445933.1:c.-400+384G>T	XM_047445933.1:c.-400+384G>A
TSGA10 transcript variant X16	XM_047445934.1:c.-400+13793=	XM_047445934.1:c.-400+13793G>T	XM_047445934.1:c.-400+13793G>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#.

2 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2732867411	Nov 08, 2017 (151)
2	TOPMED	ss4516223624	Apr 27, 2021 (155)
3	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1922998 (NC_000002.11:99757506:C:C 104063/104064, NC_000002.11:99757506:C:A 1/104064) Row 1922999 (NC_000002.11:99757506:C:C 104061/104064, NC_000002.11:99757506:C:T 3/104064)	-	Jul 13, 2019 (153)
4	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1922998 (NC_000002.11:99757506:C:C 104063/104064, NC_000002.11:99757506:C:A 1/104064) Row 1922999 (NC_000002.11:99757506:C:C 104061/104064, NC_000002.11:99757506:C:T 3/104064)	-	Jul 13, 2019 (153)
5	TopMed	NC_000002.12 - 99141044	Apr 27, 2021 (155)
6	ALFA	NC_000002.12 - 99141044	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
ss2732867411	NC_000002.11:99757506:C:A	NC_000002.12:99141043:C:A	(self)
320046503, 10298871864, ss4516223624	NC_000002.12:99141043:C:A	NC_000002.12:99141043:C:A	(self)
ss2732867411	NC_000002.11:99757506:C:T	NC_000002.12:99141043:C: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 rs1489390916

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

rs1489390916