Name: rs1491533552
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.

rs1491533552

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:102269595-102269596 (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: insC
Variation Type: Insertion
Frequency: insC=0.000008 (1/121568, GnomAD)
insC=0.00007 (1/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CUX1 : 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	=0.99993	C=0.00007	0.999858	0.000142	0
European	Sub	9690	=0.9999	C=0.0001	0.999794	0.000206	0
African	Sub	2898	=1.0000	C=0.0000	1.0	0.0	N/A
African Others	Sub	114	=1.000	C=0.000	1.0	0.0	N/A
African American	Sub	2784	=1.0000	C=0.0000	1.0	0.0	N/A
Asian	Sub	112	=1.000	C=0.000	1.0	0.0	N/A
East Asian	Sub	86	=1.00	C=0.00	1.0	0.0	N/A
Other Asian	Sub	26	=1.00	C=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	=1.000	C=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	=1.000	C=0.000	1.0	0.0	N/A
South Asian	Sub	98	=1.00	C=0.00	1.0	0.0	N/A
Other	Sub	496	=1.000	C=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
gnomAD - Genomes	Global	Study-wide	121568	- No frequency provided	insC=0.000008
gnomAD - Genomes	European	Sub	64650	- No frequency provided	insC=0.00002
gnomAD - Genomes	African	Sub	38794	- No frequency provided	insC=0.00000
gnomAD - Genomes	American	Sub	10922	- No frequency provided	insC=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	2972	- No frequency provided	insC=0.0000
gnomAD - Genomes	East Asian	Sub	2412	- No frequency provided	insC=0.0000
gnomAD - Genomes	Other	Sub	1818	- No frequency provided	insC=0.0000
Allele Frequency Aggregator	Total	Global	14050	- No frequency provided	insC=0.00007
Allele Frequency Aggregator	European	Sub	9690	- No frequency provided	insC=0.0001
Allele Frequency Aggregator	African	Sub	2898	- No frequency provided	insC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	- No frequency provided	insC=0.000
Allele Frequency Aggregator	Other	Sub	496	- No frequency provided	insC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	- No frequency provided	insC=0.000
Allele Frequency Aggregator	Asian	Sub	112	- No frequency provided	insC=0.000
Allele Frequency Aggregator	South Asian	Sub	98	- No frequency provided	insC=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 7	NC_000007.14:g.102269595_102269596insC
GRCh37.p13 chr 7 fix patch HG115_PATCH	NW_003571037.1:g.193925_193926insC
CUX1 RefSeqGene (LRG_1123)	NG_029476.2:g.458692_458693insC
GRCh37.p13 chr 7	NC_000007.13:g.101912868_101912869insC

Gene: CUX1, cut like homeobox 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CUX1 transcript variant 5	NM_001202544.3:c.1208-377… NM_001202544.3:c.1208-3771_1208-3770insC	N/A	Intron Variant
CUX1 transcript variant 6	NM_001202545.3:c.1118-377… NM_001202545.3:c.1118-3771_1118-3770insC	N/A	Intron Variant
CUX1 transcript variant 7	NM_001202546.3:c.1139-377… NM_001202546.3:c.1139-3771_1139-3770insC	N/A	Intron Variant
CUX1 transcript variant 2	NM_001913.5:c.1256-3771_1… NM_001913.5:c.1256-3771_1256-3770insC	N/A	Intron Variant
CUX1 transcript variant 3	NM_181500.4:c.1250-3771_1… NM_181500.4:c.1250-3771_1250-3770insC	N/A	Intron Variant
CUX1 transcript variant 4	NM_001202543.2:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant 1	NM_181552.4:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X18	XM_005250154.4:c.1223-377… XM_005250154.4:c.1223-3771_1223-3770insC	N/A	Intron Variant
CUX1 transcript variant X1	XM_005250150.4:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X4	XM_006715854.3:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X13	XM_011515825.3:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X12	XM_017011760.3:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X8	XM_024446668.2:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X2	XM_047419906.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X3	XM_047419907.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X5	XM_047419908.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X6	XM_047419909.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X7	XM_047419910.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X9	XM_047419911.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X10	XM_047419912.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X11	XM_047419913.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X14	XM_047419914.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X15	XM_047419915.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X16	XM_047419916.1:c.	N/A	Genic Downstream Transcript Variant
CUX1 transcript variant X17	XM_047419917.1: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	=	insC
GRCh38.p14 chr 7	NC_000007.14:g.102269595_102269596=	NC_000007.14:g.102269595_102269596insC
GRCh37.p13 chr 7 fix patch HG115_PATCH	NW_003571037.1:g.193925_193926=	NW_003571037.1:g.193925_193926insC
CUX1 RefSeqGene (LRG_1123)	NG_029476.2:g.458692_458693=	NG_029476.2:g.458692_458693insC
GRCh37.p13 chr 7	NC_000007.13:g.101912868_101912869=	NC_000007.13:g.101912868_101912869insC
CUX1 transcript variant 5	NM_001202544.1:c.1208-3768=	NM_001202544.1:c.1208-3769_1208-3768insC
CUX1 transcript variant 5	NM_001202544.3:c.1208-3770=	NM_001202544.3:c.1208-3771_1208-3770insC
CUX1 transcript variant 6	NM_001202545.1:c.1118-3768=	NM_001202545.1:c.1118-3769_1118-3768insC
CUX1 transcript variant 6	NM_001202545.3:c.1118-3770=	NM_001202545.3:c.1118-3771_1118-3770insC
CUX1 transcript variant 7	NM_001202546.1:c.1139-3768=	NM_001202546.1:c.1139-3769_1139-3768insC
CUX1 transcript variant 7	NM_001202546.3:c.1139-3770=	NM_001202546.3:c.1139-3771_1139-3770insC
CUX1 transcript variant 2	NM_001913.3:c.1256-3768=	NM_001913.3:c.1256-3769_1256-3768insC
CUX1 transcript variant 2	NM_001913.5:c.1256-3770=	NM_001913.5:c.1256-3771_1256-3770insC
CUX1 transcript variant 3	NM_181500.2:c.1250-3768=	NM_181500.2:c.1250-3769_1250-3768insC
CUX1 transcript variant 3	NM_181500.4:c.1250-3770=	NM_181500.4:c.1250-3771_1250-3770insC
CUX1 transcript variant X5	XM_005250154.1:c.1523-3768=	XM_005250154.1:c.1523-3769_1523-3768insC
CUX1 transcript variant X18	XM_005250154.4:c.1223-3770=	XM_005250154.4:c.1223-3771_1223-3770insC
CUX1 transcript variant X6	XM_005250155.1:c.1298-3768=	XM_005250155.1:c.1298-3769_1298-3768insC

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#.

1 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4169756306	Apr 26, 2021 (155)
2	gnomAD - Genomes	NC_000007.14 - 102269596	Apr 26, 2021 (155)
3	ALFA	NC_000007.14 - 102269596	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
271209298, 5878387923, ss4169756306	NC_000007.14:102269595::C	NC_000007.14:102269595::C	(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 rs1491533552

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

rs1491533552