Name: rs201422857
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.

rs201422857

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:35787109-35787119 (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: delT / dupT / dupTT
Variation Type: Indel Insertion and Deletion
Frequency: delT=0.00223 (63/28258, 14KJPN)
delT=0.00233 (39/16760, 8.3KJPN)
delT=0.00627 (99/15781, ALFA) (+ 2 more)
delT=0.015 (9/600, NorthernSweden)
delT=0.11 (4/38, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RGP1 : 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	15781	TTTTTTTTTTT=0.99373	TTTTTTTTTT=0.00627, TTTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.00000	0.987952	0.00038	0.011668	13
European	Sub	11599	TTTTTTTTTTT=0.99155	TTTTTTTTTT=0.00845, TTTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.00000	0.983776	0.000518	0.015706	10
African	Sub	2782	TTTTTTTTTTT=1.0000	TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	108	TTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
African American	Sub	2674	TTTTTTTTTTT=1.0000	TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	108	TTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	TTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	TTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	140	TTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	600	TTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	92	TTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other	Sub	460	TTTTTTTTTTT=0.998	TTTTTTTTTT=0.002, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000	0.995652	0.0	0.004348	0

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	28258	(T)₁₁=0.99777	delT=0.00223
8.3KJPN	JAPANESE	Study-wide	16760	(T)₁₁=0.99767	delT=0.00233
Allele Frequency Aggregator	Total	Global	15781	(T)₁₁=0.99373	delT=0.00627, dupT=0.00000, dupTT=0.00000
Allele Frequency Aggregator	European	Sub	11599	(T)₁₁=0.99155	delT=0.00845, dupT=0.00000, dupTT=0.00000
Allele Frequency Aggregator	African	Sub	2782	(T)₁₁=1.0000	delT=0.0000, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	600	(T)₁₁=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	460	(T)₁₁=0.998	delT=0.002, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	140	(T)₁₁=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Asian	Sub	108	(T)₁₁=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	South Asian	Sub	92	(T)₁₁=1.00	delT=0.00, dupT=0.00, dupTT=0.00
Northern Sweden	ACPOP	Study-wide	600	(T)₁₁=0.985	delT=0.015
The Danish reference pan genome	Danish	Study-wide	38	(T)₁₁=0.89	delT=0.11

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 9	NC_000009.12:g.35787119del
GRCh38.p14 chr 9	NC_000009.12:g.35787119dup
GRCh38.p14 chr 9	NC_000009.12:g.35787118_35787119dup
GRCh37.p13 chr 9	NC_000009.11:g.35787116del
GRCh37.p13 chr 9	NC_000009.11:g.35787116dup
GRCh37.p13 chr 9	NC_000009.11:g.35787115_35787116dup

Gene: RGP1, RGP1 homolog, RAB6A GEF complex partner 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RGP1 transcript	NM_001080496.3:c.	N/A	Genic Downstream Transcript Variant
RGP1 transcript variant X1	XR_007061382.1:n.	N/A	Intron Variant
RGP1 transcript variant X2	XR_007061383.1:n.	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	(T)₁₁=	delT	dupT	dupTT
GRCh38.p14 chr 9	NC_000009.12:g.35787109_35787119=	NC_000009.12:g.35787119del	NC_000009.12:g.35787119dup	NC_000009.12:g.35787118_35787119dup
GRCh37.p13 chr 9	NC_000009.11:g.35787106_35787116=	NC_000009.11:g.35787116del	NC_000009.11:g.35787116dup	NC_000009.11:g.35787115_35787116dup

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#.

13 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss498962629	May 04, 2012 (137)
2	EVA_GENOME_DK	ss1577368028	Apr 01, 2015 (144)
3	BIOINF_KMB_FNS_UNIBA	ss3646146877	Oct 12, 2018 (152)
4	EVA_DECODE	ss3723870099	Jul 13, 2019 (153)
5	EVA_DECODE	ss3723870100	Jul 13, 2019 (153)
6	ACPOP	ss3736488905	Jul 13, 2019 (153)
7	GNOMAD	ss4201070259	Apr 26, 2021 (155)
8	TOMMO_GENOMICS	ss5192993893	Apr 26, 2021 (155)
9	1000G_HIGH_COVERAGE	ss5280504670	Oct 16, 2022 (156)
10	HUGCELL_USP	ss5476708357	Oct 16, 2022 (156)
11	HUGCELL_USP	ss5476708359	Oct 16, 2022 (156)
12	TOMMO_GENOMICS	ss5736302020	Oct 16, 2022 (156)
13	EVA	ss5976601951	Oct 16, 2022 (156)
14	The Danish reference pan genome	NC_000009.11 - 35787106	Apr 26, 2020 (154)
15	gnomAD - Genomes Submission ignored due to conflicting rows: Row 324049872 (NC_000009.12:35787108::T 73/127050) Row 324049874 (NC_000009.12:35787108:T: 3068/127038)	-	Apr 26, 2021 (155)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 324049872 (NC_000009.12:35787108::T 73/127050) Row 324049874 (NC_000009.12:35787108:T: 3068/127038)	-	Apr 26, 2021 (155)
17	Northern Sweden	NC_000009.11 - 35787106	Jul 13, 2019 (153)
18	8.3KJPN	NC_000009.11 - 35787106	Apr 26, 2021 (155)
19	14KJPN	NC_000009.12 - 35787109	Oct 16, 2022 (156)
20	ALFA	NC_000009.12 - 35787109	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
1273963, 9773770, 50963200, ss498962629, ss1577368028, ss3736488905, ss5192993893, ss5976601951	NC_000009.11:35787105:T:	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTT	(self)
70139124, ss3646146877, ss3723870099, ss5280504670, ss5476708357, ss5736302020	NC_000009.12:35787108:T:	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTT	(self)
12744034280	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTT	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTT	(self)
ss4201070259, ss5476708359	NC_000009.12:35787108::T	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
12744034280	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTT	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss3723870100	NC_000009.12:35787109::T	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
12744034280	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTTT	NC_000009.12:35787108:TTTTTTTTTTT:… NC_000009.12:35787108:TTTTTTTTTTT:TTTTTTTTTTTTT	(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 rs201422857

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

rs201422857