Name: rs1491431781
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.

rs1491431781

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:112044995-112044996 (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: delAT
Variation Type: Deletion
Frequency: delAT=0.027791 (7356/264690, TOPMED)
delAT=0.026986 (3732/138296, GnomAD)
delAT=0.00060 (17/28258, 14KJPN) (+ 8 more)
delAT=0.00072 (12/16760, 8.3KJPN)
delAT=0.01757 (287/16332, ALFA)
delAT=0.0348 (223/6404, 1000G_30x)
delAT=0.0304 (152/5008, 1000G)
delAT=0.0026 (10/3854, ALSPAC)
delAT=0.0030 (11/3708, TWINSUK)
delAT=0.0005 (1/1832, Korea1K)
delAT=0.012 (12/998, GoNL)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SOX1-OT : 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	16332	AT=0.98243	=0.01757	0.967303	0.002449	0.030247	32
European	Sub	12080	AT=0.99735	=0.00265	0.994702	0.0	0.005298	0
African	Sub	2816	AT=0.9173	=0.0827	0.848011	0.013494	0.138494	6
African Others	Sub	108	AT=0.926	=0.074	0.87037	0.018519	0.111111	1
African American	Sub	2708	AT=0.9169	=0.0831	0.84712	0.013294	0.139586	6
Asian	Sub	108	AT=1.000	=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	AT=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	AT=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	AT=1.000	=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	610	AT=0.997	=0.003	0.993443	0.0	0.006557	0
South Asian	Sub	94	AT=0.94	=0.06	0.87234	0.0	0.12766	0
Other	Sub	478	AT=0.971	=0.029	0.945607	0.004184	0.050209	2

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	AT=0.972209	delAT=0.027791
gnomAD - Genomes	Global	Study-wide	138296	AT=0.973014	delAT=0.026986
gnomAD - Genomes	European	Sub	75610	AT=0.99737	delAT=0.00263
gnomAD - Genomes	African	Sub	40618	AT=0.91853	delAT=0.08147
gnomAD - Genomes	American	Sub	13524	AT=0.98713	delAT=0.01287
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	AT=0.9997	delAT=0.0003
gnomAD - Genomes	East Asian	Sub	3112	AT=0.9981	delAT=0.0019
gnomAD - Genomes	Other	Sub	2120	AT=0.9797	delAT=0.0203
14KJPN	JAPANESE	Study-wide	28258	AT=0.99940	delAT=0.00060
8.3KJPN	JAPANESE	Study-wide	16760	AT=0.99928	delAT=0.00072
Allele Frequency Aggregator	Total	Global	16332	AT=0.98243	delAT=0.01757
Allele Frequency Aggregator	European	Sub	12080	AT=0.99735	delAT=0.00265
Allele Frequency Aggregator	African	Sub	2816	AT=0.9173	delAT=0.0827
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=0.997	delAT=0.003
Allele Frequency Aggregator	Other	Sub	478	AT=0.971	delAT=0.029
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=1.000	delAT=0.000
Allele Frequency Aggregator	Asian	Sub	108	AT=1.000	delAT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	AT=0.94	delAT=0.06
1000Genomes_30x	Global	Study-wide	6404	AT=0.9652	delAT=0.0348
1000Genomes_30x	African	Sub	1786	AT=0.9059	delAT=0.0941
1000Genomes_30x	Europe	Sub	1266	AT=0.9968	delAT=0.0032
1000Genomes_30x	South Asian	Sub	1202	AT=0.9692	delAT=0.0308
1000Genomes_30x	East Asian	Sub	1170	AT=0.9974	delAT=0.0026
1000Genomes_30x	American	Sub	980	AT=0.989	delAT=0.011
1000Genomes	Global	Study-wide	5008	AT=0.9696	delAT=0.0304
1000Genomes	African	Sub	1322	AT=0.9153	delAT=0.0847
1000Genomes	East Asian	Sub	1008	AT=0.9990	delAT=0.0010
1000Genomes	Europe	Sub	1006	AT=0.9980	delAT=0.0020
1000Genomes	South Asian	Sub	978	AT=0.970	delAT=0.030
1000Genomes	American	Sub	694	AT=0.988	delAT=0.012
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AT=0.9974	delAT=0.0026
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AT=0.9970	delAT=0.0030
Korean Genome Project	KOREAN	Study-wide	1832	AT=0.9995	delAT=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AT=0.988	delAT=0.012

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.112044995_112044996del
GRCh37.p13 chr 13	NC_000013.10:g.112699309_112699310del

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

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	AT=	delAT
GRCh38.p14 chr 13	NC_000013.11:g.112044995_112044996=	NC_000013.11:g.112044995_112044996del
GRCh37.p13 chr 13	NC_000013.10:g.112699309_112699310=	NC_000013.10:g.112699309_112699310del

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, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSIP	ss947323614	Jan 10, 2018 (151)
2	EVA-GONL	ss990872475	Jan 10, 2018 (151)
3	1000GENOMES	ss1373729612	Jan 10, 2018 (151)
4	EVA_UK10K_ALSPAC	ss1707958465	Jan 10, 2018 (151)
5	EVA_UK10K_TWINSUK	ss1707958492	Jan 10, 2018 (151)
6	GNOMAD	ss2924635233	Jan 10, 2018 (151)
7	SWEGEN	ss3011742686	Jan 10, 2018 (151)
8	EVA_DECODE	ss3696169281	Jul 13, 2019 (153)
9	KHV_HUMAN_GENOMES	ss3817342666	Jul 13, 2019 (153)
10	KOGIC	ss3974396889	Apr 27, 2020 (154)
11	TOPMED	ss4961955573	Apr 26, 2021 (155)
12	TOMMO_GENOMICS	ss5211977664	Apr 26, 2021 (155)
13	1000G_HIGH_COVERAGE	ss5295272465	Oct 16, 2022 (156)
14	HUGCELL_USP	ss5489483458	Oct 16, 2022 (156)
15	1000G_HIGH_COVERAGE	ss5595079130	Oct 16, 2022 (156)
16	SANFORD_IMAGENETICS	ss5655671831	Oct 16, 2022 (156)
17	TOMMO_GENOMICS	ss5764397548	Oct 16, 2022 (156)
18	EVA	ss5926871557	Oct 16, 2022 (156)
19	EVA	ss5947122261	Oct 16, 2022 (156)
20	1000Genomes	NC_000013.10 - 112699309	Oct 12, 2018 (152)
21	1000Genomes_30x	NC_000013.11 - 112044995	Oct 16, 2022 (156)
22	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 112699309	Oct 12, 2018 (152)
23	gnomAD - Genomes	NC_000013.11 - 112044995	Apr 26, 2021 (155)
24	Genome of the Netherlands Release 5	NC_000013.10 - 112699309	Apr 27, 2020 (154)
25	Korean Genome Project	NC_000013.11 - 112044995	Apr 27, 2020 (154)
26	8.3KJPN	NC_000013.10 - 112699309	Apr 26, 2021 (155)
27	14KJPN	NC_000013.11 - 112044995	Oct 16, 2022 (156)
28	TopMed	NC_000013.11 - 112044995	Apr 26, 2021 (155)
29	UK 10K study - Twins	NC_000013.10 - 112699309	Oct 12, 2018 (152)
30	ALFA	NC_000013.11 - 112044995	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
62917768, 34967369, 15613192, 69946971, 34967369, ss947323614, ss990872475, ss1373729612, ss1707958465, ss1707958492, ss2924635233, ss3011742686, ss5211977664, ss5655671831, ss5947122261	NC_000013.10:112699308:AT:	NC_000013.11:112044994:AT:	(self)
82605065, 443582503, 30774890, 98234652, 177501231, 5224779073, ss3696169281, ss3817342666, ss3974396889, ss4961955573, ss5295272465, ss5489483458, ss5595079130, ss5764397548, ss5926871557	NC_000013.11:112044994:AT:	NC_000013.11:112044994:AT:	(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 rs1491431781

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

rs1491431781