Name: rs1476084733
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.

rs1476084733

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:39638605-39638608 (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: delC / dupC
Variation Type: Indel Insertion and Deletion
Frequency: dupC=0.000014 (2/140142, GnomAD)
delC=0.00000 (0/14050, ALFA)
dupC=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: B3GALT5 : 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	14050	CCCC=1.00000	CCC=0.00000, CCCCC=0.00000	1.0	N/A
European	Sub	9690	CCCC=1.0000	CCC=0.0000, CCCCC=0.0000	1.0	N/A
African	Sub	2898	CCCC=1.0000	CCC=0.0000, CCCCC=0.0000	1.0	N/A
African Others	Sub	114	CCCC=1.000	CCC=0.000, CCCCC=0.000	1.0	N/A
African American	Sub	2784	CCCC=1.0000	CCC=0.0000, CCCCC=0.0000	1.0	N/A
Asian	Sub	112	CCCC=1.000	CCC=0.000, CCCCC=0.000	1.0	N/A
East Asian	Sub	86	CCCC=1.00	CCC=0.00, CCCCC=0.00	1.0	N/A
Other Asian	Sub	26	CCCC=1.00	CCC=0.00, CCCCC=0.00	1.0	N/A
Latin American 1	Sub	146	CCCC=1.000	CCC=0.000, CCCCC=0.000	1.0	N/A
Latin American 2	Sub	610	CCCC=1.000	CCC=0.000, CCCCC=0.000	1.0	N/A
South Asian	Sub	98	CCCC=1.00	CCC=0.00, CCCCC=0.00	1.0	N/A
Other	Sub	496	CCCC=1.000	CCC=0.000, CCCCC=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
gnomAD - Genomes	Global	Study-wide	140142	- No frequency provided	dupC=0.000014
gnomAD - Genomes	European	Sub	75908	- No frequency provided	dupC=0.00000
gnomAD - Genomes	African	Sub	41984	- No frequency provided	dupC=0.00005
gnomAD - Genomes	American	Sub	13646	- No frequency provided	dupC=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	- No frequency provided	dupC=0.0000
gnomAD - Genomes	East Asian	Sub	3132	- No frequency provided	dupC=0.0000
gnomAD - Genomes	Other	Sub	2150	- No frequency provided	dupC=0.0000
Allele Frequency Aggregator	Total	Global	14050	(C)₄=1.00000	delC=0.00000, dupC=0.00000
Allele Frequency Aggregator	European	Sub	9690	(C)₄=1.0000	delC=0.0000, dupC=0.0000
Allele Frequency Aggregator	African	Sub	2898	(C)₄=1.0000	delC=0.0000, dupC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(C)₄=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Other	Sub	496	(C)₄=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(C)₄=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Asian	Sub	112	(C)₄=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(C)₄=1.00	delC=0.00, dupC=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 21	NC_000021.9:g.39638608del
GRCh38.p14 chr 21	NC_000021.9:g.39638608dup
GRCh37.p13 chr 21	NC_000021.8:g.41010535del
GRCh37.p13 chr 21	NC_000021.8:g.41010535dup

Gene: B3GALT5, beta-1,3-galactosyltransferase 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
B3GALT5 transcript variant 6	NM_001278650.2:c.-160-211… NM_001278650.2:c.-160-21145del	N/A	Intron Variant
B3GALT5 transcript variant 7	NM_001356336.2:c.-391-778… NM_001356336.2:c.-391-7784del	N/A	Intron Variant
B3GALT5 transcript variant 8	NM_001356338.2:c.	N/A	Genic Upstream Transcript Variant
B3GALT5 transcript variant 9	NM_001356339.2:c.	N/A	Genic Upstream Transcript Variant
B3GALT5 transcript variant 1	NM_006057.3:c.	N/A	Genic Upstream Transcript Variant
B3GALT5 transcript variant 2	NM_033170.3:c.	N/A	Genic Upstream Transcript Variant
B3GALT5 transcript variant 3	NM_033171.3:c.	N/A	Genic Upstream Transcript Variant
B3GALT5 transcript variant 4	NM_033172.3:c.	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	(C)₄=	delC	dupC
GRCh38.p14 chr 21	NC_000021.9:g.39638605_39638608=	NC_000021.9:g.39638608del	NC_000021.9:g.39638608dup
GRCh37.p13 chr 21	NC_000021.8:g.41010532_41010535=	NC_000021.8:g.41010535del	NC_000021.8:g.41010535dup
B3GALT5 transcript variant 6	NM_001278650.1:c.-160-21148=	NM_001278650.1:c.-160-21145del	NM_001278650.1:c.-160-21145dup
B3GALT5 transcript variant 6	NM_001278650.2:c.-160-21148=	NM_001278650.2:c.-160-21145del	NM_001278650.2:c.-160-21145dup
B3GALT5 transcript variant 7	NM_001356336.2:c.-391-7787=	NM_001356336.2:c.-391-7784del	NM_001356336.2:c.-391-7784dup
B3GALT5 transcript variant X1	XM_005260912.1:c.-391-7787=	XM_005260912.1:c.-391-7784del	XM_005260912.1:c.-391-7784dup

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#.

3 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2971952833	Nov 08, 2017 (151)
2	TOPMED	ss5102113723	Apr 27, 2021 (155)
3	TOPMED	ss5102113724	Apr 27, 2021 (155)
4	gnomAD - Genomes	NC_000021.9 - 39638605	Apr 27, 2021 (155)
5	TopMed Submission ignored due to conflicting rows: Row 377222669 (NC_000021.9:39638604::C 6/264690) Row 377222670 (NC_000021.9:39638604:C: 5/264690)	-	Apr 27, 2021 (155)
6	TopMed Submission ignored due to conflicting rows: Row 377222669 (NC_000021.9:39638604::C 6/264690) Row 377222670 (NC_000021.9:39638604:C: 5/264690)	-	Apr 27, 2021 (155)
7	ALFA	NC_000021.9 - 39638605	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
ss5102113724	NC_000021.9:39638604:C:	NC_000021.9:39638604:CCCC:CCC	(self)
4580980645	NC_000021.9:39638604:CCCC:CCC	NC_000021.9:39638604:CCCC:CCC	(self)
ss2971952833	NC_000021.8:41010531::C	NC_000021.9:39638604:CCCC:CCCCC	(self)
563594541, ss5102113723	NC_000021.9:39638604::C	NC_000021.9:39638604:CCCC:CCCCC	(self)
4580980645	NC_000021.9:39638604:CCCC:CCCCC	NC_000021.9:39638604:CCCC:CCCCC	(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 rs1476084733

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

rs1476084733