Name: rs1491443955
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.

rs1491443955

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:64239105 (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: dupG / insGGG
Variation Type: Indel Insertion and Deletion
Frequency: dupG=0.00179 (40/22320, 14KJPN)
dupG=0.00050 (8/15942, GnomAD)
dupG=0.00333 (40/12006, 8.3KJPN) (+ 1 more)
dupG=0.00000 (0/11860, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: UBE2U : 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	HWEP
Total	Global	11860	G=1.00000	GG=0.00000	1.0	N/A
European	Sub	7616	G=1.0000	GG=0.0000	1.0	N/A
African	Sub	2816	G=1.0000	GG=0.0000	1.0	N/A
African Others	Sub	108	G=1.000	GG=0.000	1.0	N/A
African American	Sub	2708	G=1.0000	GG=0.0000	1.0	N/A
Asian	Sub	108	G=1.000	GG=0.000	1.0	N/A
East Asian	Sub	84	G=1.00	GG=0.00	1.0	N/A
Other Asian	Sub	24	G=1.00	GG=0.00	1.0	N/A
Latin American 1	Sub	146	G=1.000	GG=0.000	1.0	N/A
Latin American 2	Sub	610	G=1.000	GG=0.000	1.0	N/A
South Asian	Sub	94	G=1.00	GG=0.00	1.0	N/A
Other	Sub	470	G=1.000	GG=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
14KJPN	JAPANESE	Study-wide	22320	- No frequency provided	dupG=0.00179
gnomAD - Genomes	Global	Study-wide	15942	- No frequency provided	dupG=0.00050
gnomAD - Genomes	European	Sub	10864	- No frequency provided	dupG=0.00037
gnomAD - Genomes	African	Sub	3082	- No frequency provided	dupG=0.0013
gnomAD - Genomes	American	Sub	1188	- No frequency provided	dupG=0.0000
gnomAD - Genomes	Ashkenazi Jewish	Sub	384	- No frequency provided	dupG=0.000
gnomAD - Genomes	Other	Sub	218	- No frequency provided	dupG=0.000
gnomAD - Genomes	East Asian	Sub	206	- No frequency provided	dupG=0.000
8.3KJPN	JAPANESE	Study-wide	12006	- No frequency provided	dupG=0.00333
Allele Frequency Aggregator	Total	Global	11860	G=1.00000	dupG=0.00000
Allele Frequency Aggregator	European	Sub	7616	G=1.0000	dupG=0.0000
Allele Frequency Aggregator	African	Sub	2816	G=1.0000	dupG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	dupG=0.000
Allele Frequency Aggregator	Other	Sub	470	G=1.000	dupG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	dupG=0.000
Allele Frequency Aggregator	Asian	Sub	108	G=1.000	dupG=0.000
Allele Frequency Aggregator	South Asian	Sub	94	G=1.00	dupG=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 1	NC_000001.11:g.64239105dup
GRCh38.p14 chr 1	NC_000001.11:g.64239105_64239106insGGG
GRCh37.p13 chr 1	NC_000001.10:g.64704788dup
GRCh37.p13 chr 1	NC_000001.10:g.64704788_64704789insGGG

Gene: UBE2U, ubiquitin conjugating enzyme E2 U (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2U transcript variant 1	NM_001366232.2:c.596-2547… NM_001366232.2:c.596-2547dup	N/A	Intron Variant
UBE2U transcript variant 2	NM_001366233.2:c.593-2547… NM_001366233.2:c.593-2547dup	N/A	Intron Variant
UBE2U transcript variant 3	NM_001366234.2:c.458-2547… NM_001366234.2:c.458-2547dup	N/A	Intron Variant
UBE2U transcript variant 5	NM_001366235.1:c.507-2547… NM_001366235.1:c.507-2547dup	N/A	Intron Variant
UBE2U transcript variant 4	NM_152489.3:c.596-2547dup	N/A	Intron Variant
UBE2U transcript variant 6	NR_158768.1:n.	N/A	Intron Variant
UBE2U transcript variant 7	NR_158769.2:n.	N/A	Intron Variant
UBE2U transcript variant X1	XM_006710379.4:c.500-2547… XM_006710379.4:c.500-2547dup	N/A	Intron Variant
UBE2U transcript variant X2	XM_017000379.2:c.218-2547… XM_017000379.2:c.218-2547dup	N/A	Intron Variant
UBE2U transcript variant X3	XM_017000380.2:c.218-2547… XM_017000380.2:c.218-2547dup	N/A	Intron Variant
UBE2U transcript variant X4	XM_017000381.2:c.218-2547… XM_017000381.2:c.218-2547dup	N/A	Intron Variant
UBE2U transcript variant X5	XM_017000382.2:c.218-2547… XM_017000382.2:c.218-2547dup	N/A	Intron Variant
UBE2U transcript variant X6	XM_017000383.2:c.140-2547… XM_017000383.2:c.140-2547dup	N/A	Intron Variant
UBE2U transcript variant X7	XM_017000384.2:c.140-2547… XM_017000384.2:c.140-2547dup	N/A	Intron 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	G=	dupG	insGGG
GRCh38.p14 chr 1	NC_000001.11:g.64239105=	NC_000001.11:g.64239105dup	NC_000001.11:g.64239105_64239106insGGG
GRCh37.p13 chr 1	NC_000001.10:g.64704788=	NC_000001.10:g.64704788dup	NC_000001.10:g.64704788_64704789insGGG
UBE2U transcript variant 1	NM_001366232.2:c.596-2547=	NM_001366232.2:c.596-2547dup	NM_001366232.2:c.596-2547_596-2546insGGG
UBE2U transcript variant 2	NM_001366233.2:c.593-2547=	NM_001366233.2:c.593-2547dup	NM_001366233.2:c.593-2547_593-2546insGGG
UBE2U transcript variant 3	NM_001366234.2:c.458-2547=	NM_001366234.2:c.458-2547dup	NM_001366234.2:c.458-2547_458-2546insGGG
UBE2U transcript variant 5	NM_001366235.1:c.507-2547=	NM_001366235.1:c.507-2547dup	NM_001366235.1:c.507-2547_507-2546insGGG
UBE2U transcript	NM_152489.1:c.596-2547=	NM_152489.1:c.596-2547dup	NM_152489.1:c.596-2547_596-2546insGGG
UBE2U transcript variant 4	NM_152489.3:c.596-2547=	NM_152489.3:c.596-2547dup	NM_152489.3:c.596-2547_596-2546insGGG
UBE2U transcript variant X1	XM_005270498.1:c.596-2547=	XM_005270498.1:c.596-2547dup	XM_005270498.1:c.596-2547_596-2546insGGG
UBE2U transcript variant X2	XM_005270499.1:c.507-2547=	XM_005270499.1:c.507-2547dup	XM_005270499.1:c.507-2547_507-2546insGGG
UBE2U transcript variant X1	XM_006710379.4:c.500-2547=	XM_006710379.4:c.500-2547dup	XM_006710379.4:c.500-2547_500-2546insGGG
UBE2U transcript variant X2	XM_017000379.2:c.218-2547=	XM_017000379.2:c.218-2547dup	XM_017000379.2:c.218-2547_218-2546insGGG
UBE2U transcript variant X3	XM_017000380.2:c.218-2547=	XM_017000380.2:c.218-2547dup	XM_017000380.2:c.218-2547_218-2546insGGG
UBE2U transcript variant X4	XM_017000381.2:c.218-2547=	XM_017000381.2:c.218-2547dup	XM_017000381.2:c.218-2547_218-2546insGGG
UBE2U transcript variant X5	XM_017000382.2:c.218-2547=	XM_017000382.2:c.218-2547dup	XM_017000382.2:c.218-2547_218-2546insGGG
UBE2U transcript variant X6	XM_017000383.2:c.140-2547=	XM_017000383.2:c.140-2547dup	XM_017000383.2:c.140-2547_140-2546insGGG
UBE2U transcript variant X7	XM_017000384.2:c.140-2547=	XM_017000384.2:c.140-2547dup	XM_017000384.2:c.140-2547_140-2546insGGG

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#.

4 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss3994770709	Apr 25, 2021 (155)
2	TOMMO_GENOMICS	ss5144238770	Apr 25, 2021 (155)
3	HUGCELL_USP	ss5443534825	Oct 12, 2022 (156)
4	TOMMO_GENOMICS	ss5669093519	Oct 12, 2022 (156)
5	gnomAD - Genomes	NC_000001.11 - 64239105	Apr 25, 2021 (155)
6	8.3KJPN	NC_000001.10 - 64704788	Apr 25, 2021 (155)
7	14KJPN	NC_000001.11 - 64239105	Oct 12, 2022 (156)
8	ALFA	NC_000001.11 - 64239105	Apr 25, 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
2208077, ss5144238770	NC_000001.10:64704787::G	NC_000001.11:64239104:G:GG	(self)
13249585, 2930623, ss3994770709, ss5669093519	NC_000001.11:64239104::G	NC_000001.11:64239104:G:GG	(self)
5067456377	NC_000001.11:64239104:G:GG	NC_000001.11:64239104:G:GG	(self)
ss5443534825	NC_000001.11:64239104::GGG	NC_000001.11:64239104:G:GGGG

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1491443955

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

rs1491443955