Name: rs35968550
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.

rs35968550

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:20172501-20172502 (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: delCA
Variation Type: Deletion
Frequency: delCA=0.00120 (34/28220, 14KJPN)
delCA=0.00051 (6/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SGO1 : Intron Variant
SGO1-AS1 : 2KB Upstream 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	11862	CA=0.99949	=0.00051	0.998988	0.001012	0
European	Sub	7618	CA=1.0000	=0.0000	1.0	0.0	N/A
African	Sub	2816	CA=0.9982	=0.0018	0.996449	0.003551	0
African Others	Sub	108	CA=1.000	=0.000	1.0	0.0	N/A
African American	Sub	2708	CA=0.9982	=0.0018	0.996307	0.003693	0
Asian	Sub	108	CA=0.991	=0.009	0.981481	0.018519	0
East Asian	Sub	84	CA=0.99	=0.01	0.97619	0.02381	0
Other Asian	Sub	24	CA=1.00	=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CA=1.000	=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CA=1.000	=0.000	1.0	0.0	N/A
South Asian	Sub	94	CA=1.00	=0.00	1.0	0.0	N/A
Other	Sub	470	CA=1.000	=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
14KJPN	JAPANESE	Study-wide	28220	CA=0.99880	delCA=0.00120
Allele Frequency Aggregator	Total	Global	11862	CA=0.99949	delCA=0.00051
Allele Frequency Aggregator	European	Sub	7618	CA=1.0000	delCA=0.0000
Allele Frequency Aggregator	African	Sub	2816	CA=0.9982	delCA=0.0018
Allele Frequency Aggregator	Latin American 2	Sub	610	CA=1.000	delCA=0.000
Allele Frequency Aggregator	Other	Sub	470	CA=1.000	delCA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CA=1.000	delCA=0.000
Allele Frequency Aggregator	Asian	Sub	108	CA=0.991	delCA=0.009
Allele Frequency Aggregator	South Asian	Sub	94	CA=1.00	delCA=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 3	NC_000003.12:g.20172501_20172502del
GRCh37.p13 chr 3	NC_000003.11:g.20213993_20213994del
SGO1 RefSeqGene	NG_042062.1:g.18730_18731del

Gene: SGO1, shugoshin 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SGO1 transcript variant A1	NM_001012409.4:c.1283-127… NM_001012409.4:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1F	NM_001012410.5:c.1283-127… NM_001012410.5:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1C	NM_001012411.4:c.527-1270… NM_001012411.4:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1H	NM_001012412.5:c.527-1270… NM_001012412.5:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1B	NM_001012413.4:c.476-1270… NM_001012413.4:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant 1	NM_001199251.3:c.1283-127… NM_001199251.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1E	NM_001199252.3:c.1283-127… NM_001199252.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1D	NM_001199253.3:c.527-1270… NM_001199253.3:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1G	NM_001199254.3:c.527-1270… NM_001199254.3:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1A	NM_001199255.3:c.476-1270… NM_001199255.3:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1K	NM_001199256.3:c.476-1270… NM_001199256.3:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant Sgo1J	NM_001199257.3:c.526+2503… NM_001199257.3:c.526+2503_526+2504del	N/A	Intron Variant
SGO1 transcript variant Sgo1L	NM_138484.5:c.476-1270_47… NM_138484.5:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant 14	NR_131179.2:n.	N/A	Intron Variant
SGO1 transcript variant 15	NR_131180.2:n.	N/A	Intron Variant
SGO1 transcript variant X1	XM_011533373.3:c.1283-127… XM_011533373.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant X3	XM_011533375.3:c.1283-127… XM_011533375.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant X2	XM_011533376.3:c.1283-127… XM_011533376.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant X4	XM_011533377.3:c.1283-127… XM_011533377.3:c.1283-1270_1283-1269del	N/A	Intron Variant
SGO1 transcript variant X5	XM_047447486.1:c.527-1270… XM_047447486.1:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant X6	XM_047447487.1:c.476-1270… XM_047447487.1:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant X7	XM_047447488.1:c.527-1270… XM_047447488.1:c.527-1270_527-1269del	N/A	Intron Variant
SGO1 transcript variant X8	XM_047447489.1:c.476-1270… XM_047447489.1:c.476-1270_476-1269del	N/A	Intron Variant
SGO1 transcript variant X9	XM_047447490.1:c.476-1270… XM_047447490.1:c.476-1270_476-1269del	N/A	Intron Variant

Gene: SGO1-AS1, SGO1 antisense RNA 1 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SGO1-AS1 transcript	NR_132785.1: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	CA=	delCA
GRCh38.p14 chr 3	NC_000003.12:g.20172501_20172502=	NC_000003.12:g.20172501_20172502del
GRCh37.p13 chr 3	NC_000003.11:g.20213993_20213994=	NC_000003.11:g.20213993_20213994del
SGO1 RefSeqGene	NG_042062.1:g.18730_18731=	NG_042062.1:g.18730_18731del
SGOL1 transcript variant A1	NM_001012409.2:c.1283-1269=	NM_001012409.2:c.1283-1270_1283-1269del
SGO1 transcript variant A1	NM_001012409.4:c.1283-1269=	NM_001012409.4:c.1283-1270_1283-1269del
SGOL1 transcript variant A2	NM_001012410.3:c.1283-1269=	NM_001012410.3:c.1283-1270_1283-1269del
SGO1 transcript variant Sgo1F	NM_001012410.5:c.1283-1269=	NM_001012410.5:c.1283-1270_1283-1269del
SGOL1 transcript variant B1	NM_001012411.2:c.527-1269=	NM_001012411.2:c.527-1270_527-1269del
SGO1 transcript variant Sgo1C	NM_001012411.4:c.527-1269=	NM_001012411.4:c.527-1270_527-1269del
SGOL1 transcript variant B2	NM_001012412.3:c.527-1269=	NM_001012412.3:c.527-1270_527-1269del
SGO1 transcript variant Sgo1H	NM_001012412.5:c.527-1269=	NM_001012412.5:c.527-1270_527-1269del
SGOL1 transcript variant C1	NM_001012413.2:c.476-1269=	NM_001012413.2:c.476-1270_476-1269del
SGO1 transcript variant Sgo1B	NM_001012413.4:c.476-1269=	NM_001012413.4:c.476-1270_476-1269del
SGOL1 transcript variant A3	NM_001199251.1:c.1283-1269=	NM_001199251.1:c.1283-1270_1283-1269del
SGO1 transcript variant 1	NM_001199251.3:c.1283-1269=	NM_001199251.3:c.1283-1270_1283-1269del
SGOL1 transcript variant A4	NM_001199252.1:c.1283-1269=	NM_001199252.1:c.1283-1270_1283-1269del
SGO1 transcript variant Sgo1E	NM_001199252.3:c.1283-1269=	NM_001199252.3:c.1283-1270_1283-1269del
SGOL1 transcript variant B3	NM_001199253.1:c.527-1269=	NM_001199253.1:c.527-1270_527-1269del
SGO1 transcript variant Sgo1D	NM_001199253.3:c.527-1269=	NM_001199253.3:c.527-1270_527-1269del
SGOL1 transcript variant B4	NM_001199254.1:c.527-1269=	NM_001199254.1:c.527-1270_527-1269del
SGO1 transcript variant Sgo1G	NM_001199254.3:c.527-1269=	NM_001199254.3:c.527-1270_527-1269del
SGOL1 transcript variant C3	NM_001199255.1:c.476-1269=	NM_001199255.1:c.476-1270_476-1269del
SGO1 transcript variant Sgo1A	NM_001199255.3:c.476-1269=	NM_001199255.3:c.476-1270_476-1269del
SGOL1 transcript variant C4	NM_001199256.1:c.476-1269=	NM_001199256.1:c.476-1270_476-1269del
SGO1 transcript variant Sgo1K	NM_001199256.3:c.476-1269=	NM_001199256.3:c.476-1270_476-1269del
SGOL1 transcript variant D1	NM_001199257.1:c.526+2504=	NM_001199257.1:c.526+2503_526+2504del
SGO1 transcript variant Sgo1J	NM_001199257.3:c.526+2504=	NM_001199257.3:c.526+2503_526+2504del
SGOL1 transcript variant C2	NM_138484.3:c.476-1269=	NM_138484.3:c.476-1270_476-1269del
SGO1 transcript variant Sgo1L	NM_138484.5:c.476-1269=	NM_138484.5:c.476-1270_476-1269del
SGO1 transcript variant X1	XM_011533373.3:c.1283-1269=	XM_011533373.3:c.1283-1270_1283-1269del
SGO1 transcript variant X3	XM_011533375.3:c.1283-1269=	XM_011533375.3:c.1283-1270_1283-1269del
SGO1 transcript variant X2	XM_011533376.3:c.1283-1269=	XM_011533376.3:c.1283-1270_1283-1269del
SGO1 transcript variant X4	XM_011533377.3:c.1283-1269=	XM_011533377.3:c.1283-1270_1283-1269del
SGO1 transcript variant X5	XM_047447486.1:c.527-1269=	XM_047447486.1:c.527-1270_527-1269del
SGO1 transcript variant X6	XM_047447487.1:c.476-1269=	XM_047447487.1:c.476-1270_476-1269del
SGO1 transcript variant X7	XM_047447488.1:c.527-1269=	XM_047447488.1:c.527-1270_527-1269del
SGO1 transcript variant X8	XM_047447489.1:c.476-1269=	XM_047447489.1:c.476-1270_476-1269del
SGO1 transcript variant X9	XM_047447490.1:c.476-1269=	XM_047447490.1:c.476-1270_476-1269del

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#.

2 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSIP	ss947082045	Aug 21, 2014 (144)
2	TOMMO_GENOMICS	ss5689437016	Oct 13, 2022 (156)
3	14KJPN	NC_000003.12 - 20172501	Oct 13, 2022 (156)
4	ALFA	NC_000003.12 - 20172501	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).

Associated ID	History Updated (Build)
rs541840037	Apr 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss947082045	NC_000003.11:20213992:CA:	NC_000003.12:20172500:CA:	(self)
23274120, 8286655713, ss5689437016	NC_000003.12:20172500:CA:	NC_000003.12:20172500:CA:	(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 rs35968550

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

rs35968550