Name: rs1491303900
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.

rs1491303900

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:112050258 (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: dupA / insAA / insAAA / ins(A)₄ / …
dupA / insAA / insAAA / ins(A)₄ / ins(A)₅ / ins(A)₆ / ins(A)₈ / ins(A)₉ / ins(A)₁₁ / ins(A)₁₂ / ins(A)₁₆ / ins(A)₁₈ / ins(A)₂₂ / ins(A)₂₅
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.00062 (10/16224, 8.3KJPN)
dupA=0.00000 (0/11326, ALFA)
insAA=0.00000 (0/11326, ALFA) (+ 3 more)
insAAA=0.00000 (0/11326, ALFA)
ins(A)₄=0.00000 (0/11326, ALFA)
ins(A)₆=0.00000 (0/11326, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SOX1-OT : Intron Variant
LOC124900341 : 2KB Upstream Variant
Publications: 0 citations
Genomic View: See rs on genome

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
8.3KJPN	JAPANESE	Study-wide	16224	- No frequency provided	dupA=0.00062
Allele Frequency Aggregator	Total	Global	11326	A=1.00000	dupA=0.00000, insAA=0.00000, insAAA=0.00000, ins(A)₄=0.00000, ins(A)₆=0.00000
Allele Frequency Aggregator	European	Sub	7592	A=1.0000	dupA=0.0000, insAA=0.0000, insAAA=0.0000, ins(A)₄=0.0000, ins(A)₆=0.0000
Allele Frequency Aggregator	African	Sub	2364	A=1.0000	dupA=0.0000, insAA=0.0000, insAAA=0.0000, ins(A)₄=0.0000, ins(A)₆=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	594	A=1.000	dupA=0.000, insAA=0.000, insAAA=0.000, ins(A)₄=0.000, ins(A)₆=0.000
Allele Frequency Aggregator	Other	Sub	434	A=1.000	dupA=0.000, insAA=0.000, insAAA=0.000, ins(A)₄=0.000, ins(A)₆=0.000
Allele Frequency Aggregator	Latin American 1	Sub	140	A=1.000	dupA=0.000, insAA=0.000, insAAA=0.000, ins(A)₄=0.000, ins(A)₆=0.000
Allele Frequency Aggregator	Asian	Sub	108	A=1.000	dupA=0.000, insAA=0.000, insAAA=0.000, ins(A)₄=0.000, ins(A)₆=0.000
Allele Frequency Aggregator	South Asian	Sub	94	A=1.00	dupA=0.00, insAA=0.00, insAAA=0.00, ins(A)₄=0.00, ins(A)₆=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 13	NC_000013.11:g.112050258dup
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAAAAAA
GRCh38.p14 chr 13	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572dup
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAAAAAAAAA

Gene: SOX1-OT, SOX1 overlapping transcript (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SOX1-OT transcript variant 1	NR_120392.1:n.	N/A	Intron Variant
SOX1-OT transcript variant 2	NR_120394.1:n.	N/A	Genic Upstream Transcript Variant

Gene: LOC124900341, uncharacterized LOC124900341 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124900341 transcript	XR_007063953.1:n.	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	A=	dupA	insAA	insAAA	ins(A)₄	ins(A)₅	ins(A)₆	ins(A)₈	ins(A)₉	ins(A)₁₁	ins(A)₁₂	ins(A)₁₆	ins(A)₁₈	ins(A)₂₂	ins(A)₂₅
GRCh38.p14 chr 13	NC_000013.11:g.112050258=	NC_000013.11:g.112050258dup	NC_000013.11:g.112050258_112050259insAA	NC_000013.11:g.112050258_112050259insAAA	NC_000013.11:g.112050258_112050259insAAAA	NC_000013.11:g.112050258_112050259insAAAAA	NC_000013.11:g.112050258_112050259insAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAAAAAA	NC_000013.11:g.112050258_112050259insAAAAAAAAAAAAAAAAAAAAAAAAA
GRCh37.p13 chr 13	NC_000013.10:g.112704572=	NC_000013.10:g.112704572dup	NC_000013.10:g.112704572_112704573insAA	NC_000013.10:g.112704572_112704573insAAA	NC_000013.10:g.112704572_112704573insAAAA	NC_000013.10:g.112704572_112704573insAAAAA	NC_000013.10:g.112704572_112704573insAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAAAAAA	NC_000013.10:g.112704572_112704573insAAAAAAAAAAAAAAAAAAAAAAAAA

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#.

19 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4273559945	Apr 26, 2021 (155)
2	GNOMAD	ss4273559946	Apr 26, 2021 (155)
3	GNOMAD	ss4273559947	Apr 26, 2021 (155)
4	GNOMAD	ss4273559948	Apr 26, 2021 (155)
5	GNOMAD	ss4273559949	Apr 26, 2021 (155)
6	GNOMAD	ss4273559950	Apr 26, 2021 (155)
7	GNOMAD	ss4273559951	Apr 26, 2021 (155)
8	GNOMAD	ss4273559952	Apr 26, 2021 (155)
9	GNOMAD	ss4273559953	Apr 26, 2021 (155)
10	GNOMAD	ss4273559954	Apr 26, 2021 (155)
11	GNOMAD	ss4273559955	Apr 26, 2021 (155)
12	GNOMAD	ss4273559956	Apr 26, 2021 (155)
13	GNOMAD	ss4273559957	Apr 26, 2021 (155)
14	TOMMO_GENOMICS	ss5211977846	Apr 26, 2021 (155)
15	1000G_HIGH_COVERAGE	ss5295272616	Oct 16, 2022 (156)
16	HUGCELL_USP	ss5489483603	Oct 16, 2022 (156)
17	HUGCELL_USP	ss5489483604	Oct 16, 2022 (156)
18	TOMMO_GENOMICS	ss5764397787	Oct 16, 2022 (156)
19	TOMMO_GENOMICS	ss5764397788	Oct 16, 2022 (156)
20	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
21	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
22	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
23	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
24	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
25	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
26	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
27	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
28	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
29	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
30	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
31	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
32	gnomAD - Genomes Submission ignored due to conflicting rows: Row 443583591 (NC_000013.11:112050257::A 1138/33114) Row 443583592 (NC_000013.11:112050257::AA 1880/33206) Row 443583593 (NC_000013.11:112050257::AAA 188/33332)...	-	Apr 26, 2021 (155)
33	8.3KJPN	NC_000013.10 - 112704572	Apr 26, 2021 (155)
34	14KJPN Submission ignored due to conflicting rows: Row 98234891 (NC_000013.11:112050257::A 9/27982) Row 98234892 (NC_000013.11:112050257::AA 2/27982)	-	Oct 16, 2022 (156)
35	14KJPN Submission ignored due to conflicting rows: Row 98234891 (NC_000013.11:112050257::A 9/27982) Row 98234892 (NC_000013.11:112050257::AA 2/27982)	-	Oct 16, 2022 (156)
36	ALFA	NC_000013.11 - 112050258	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
69947153, ss5211977846	NC_000013.10:112704571::A	NC_000013.11:112050257:A:AA	(self)
ss4273559945, ss5489483603, ss5764397787	NC_000013.11:112050257::A	NC_000013.11:112050257:A:AA	(self)
1259099346	NC_000013.11:112050257:A:AA	NC_000013.11:112050257:A:AA	(self)
ss4273559946, ss5489483604, ss5764397788	NC_000013.11:112050257::AA	NC_000013.11:112050257:A:AAA	(self)
1259099346	NC_000013.11:112050257:A:AAA	NC_000013.11:112050257:A:AAA	(self)
ss4273559947, ss5295272616	NC_000013.11:112050257::AAA	NC_000013.11:112050257:A:AAAA	(self)
1259099346	NC_000013.11:112050257:A:AAAA	NC_000013.11:112050257:A:AAAA	(self)
ss4273559948	NC_000013.11:112050257::AAAA	NC_000013.11:112050257:A:AAAAA	(self)
1259099346	NC_000013.11:112050257:A:AAAAA	NC_000013.11:112050257:A:AAAAA	(self)
ss4273559949	NC_000013.11:112050257::AAAAA	NC_000013.11:112050257:A:AAAAAA	(self)
1259099346	NC_000013.11:112050257:A:AAAAAAA	NC_000013.11:112050257:A:AAAAAAA	(self)
ss4273559950	NC_000013.11:112050257::AAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA	(self)
ss4273559951	NC_000013.11:112050257::AAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAAA	(self)
ss4273559952	NC_000013.11:112050257::AAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAA	(self)
ss4273559953	NC_000013.11:112050257::AAAAAAAAAA… NC_000013.11:112050257::AAAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAAA	(self)
ss4273559954	NC_000013.11:112050257::AAAAAAAAAA… NC_000013.11:112050257::AAAAAAAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAAAAAAA	(self)
ss4273559955	NC_000013.11:112050257::AAAAAAAAAA… NC_000013.11:112050257::AAAAAAAAAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAAAAAAAAA	(self)
ss4273559956	NC_000013.11:112050257::AAAAAAAAAA… NC_000013.11:112050257::AAAAAAAAAAAAAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAAAAAAAAAAAAA	(self)
ss4273559957	NC_000013.11:112050257::AAAAAAAAAA… NC_000013.11:112050257::AAAAAAAAAAAAAAAAAAAAAAAAA	NC_000013.11:112050257:A:AAAAAAAAA… NC_000013.11:112050257:A:AAAAAAAAAAAAAAAAAAAAAAAAAA	(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 rs1491303900

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

rs1491303900