Name: rs1491194692
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.

rs1491194692

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:20727284-20727287 (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
Variation Type: Indel Insertion and Deletion
Frequency: dupG=0.000004 (1/264690, TOPMED)
dupG=0.000004 (1/251038, GnomAD_exome)
dupG=0.00000 (0/10680, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PACRGL : Splice Acceptor 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	10680	GGGG=1.00000	GGGGG=0.00000	1.0	N/A
European	Sub	6962	GGGG=1.0000	GGGGG=0.0000	1.0	N/A
African	Sub	2294	GGGG=1.0000	GGGGG=0.0000	1.0	N/A
African Others	Sub	84	GGGG=1.00	GGGGG=0.00	1.0	N/A
African American	Sub	2210	GGGG=1.0000	GGGGG=0.0000	1.0	N/A
Asian	Sub	108	GGGG=1.000	GGGGG=0.000	1.0	N/A
East Asian	Sub	84	GGGG=1.00	GGGGG=0.00	1.0	N/A
Other Asian	Sub	24	GGGG=1.00	GGGGG=0.00	1.0	N/A
Latin American 1	Sub	146	GGGG=1.000	GGGGG=0.000	1.0	N/A
Latin American 2	Sub	610	GGGG=1.000	GGGGG=0.000	1.0	N/A
South Asian	Sub	94	GGGG=1.00	GGGGG=0.00	1.0	N/A
Other	Sub	466	GGGG=1.000	GGGGG=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
TopMed	Global	Study-wide	264690	- No frequency provided	dupG=0.000004
gnomAD - Exomes	Global	Study-wide	251038	- No frequency provided	dupG=0.000004
gnomAD - Exomes	European	Sub	135066	- No frequency provided	dupG=0.000007
gnomAD - Exomes	Asian	Sub	49000	- No frequency provided	dupG=0.00000
gnomAD - Exomes	American	Sub	34526	- No frequency provided	dupG=0.00000
gnomAD - Exomes	African	Sub	16254	- No frequency provided	dupG=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	10066	- No frequency provided	dupG=0.00000
gnomAD - Exomes	Other	Sub	6126	- No frequency provided	dupG=0.0000
Allele Frequency Aggregator	Total	Global	10680	(G)₄=1.00000	dupG=0.00000
Allele Frequency Aggregator	European	Sub	6962	(G)₄=1.0000	dupG=0.0000
Allele Frequency Aggregator	African	Sub	2294	(G)₄=1.0000	dupG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(G)₄=1.000	dupG=0.000
Allele Frequency Aggregator	Other	Sub	466	(G)₄=1.000	dupG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(G)₄=1.000	dupG=0.000
Allele Frequency Aggregator	Asian	Sub	108	(G)₄=1.000	dupG=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(G)₄=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 4	NC_000004.12:g.20727287dup
GRCh37.p13 chr 4	NC_000004.11:g.20728910dup
KCNIP4 RefSeqGene	NG_052969.1:g.1226468dup

Gene: PACRGL, parkin coregulated like (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PACRGL transcript variant 2	NM_001130727.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 3	NM_001258345.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 4	NM_001258346.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 6	NM_001317849.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 7	NM_001330745.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 8	NM_001330746.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 9	NM_001330747.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 10	NM_001330748.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 1	NM_145048.5:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant 5	NR_047661.3:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant 11	NR_133933.2:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X3	XM_011513784.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X4	XM_011513786.4:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X22	XM_011513804.2:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X24	XM_011513805.4:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X14	XM_017007747.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X16	XM_017007748.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X31	XM_017007759.3:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X5	XM_047449617.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X6	XM_047449618.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X9	XM_047449619.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X10	XM_047449620.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X12	XM_047449621.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X15	XM_047449622.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X17	XM_047449623.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X19	XM_047449624.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X20	XM_047449625.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X21	XM_047449626.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X23	XM_047449627.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X27	XM_047449628.1:c.	N/A	Splice Acceptor Variant
PACRGL transcript variant X13	XR_001741142.3:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X7	XR_007096362.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X11	XR_007096363.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X18	XR_007096364.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X25	XR_007096365.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X26	XR_007096366.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X28	XR_007096367.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X29	XR_007096368.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X30	XR_007096369.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X32	XR_007096370.1:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X1	XR_925302.3:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X2	XR_925303.4:n.	N/A	Splice Acceptor Variant
PACRGL transcript variant X8	XR_925306.3:n.	N/A	Splice Acceptor 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)₄=	dupG
GRCh38.p14 chr 4	NC_000004.12:g.20727284_20727287=	NC_000004.12:g.20727287dup
GRCh37.p13 chr 4	NC_000004.11:g.20728907_20728910=	NC_000004.11:g.20728910dup
KCNIP4 RefSeqGene	NG_052969.1:g.1226465_1226468=	NG_052969.1:g.1226468dup

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, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2734438506	Jan 10, 2018 (151)
2	TOPMED	ss4605448834	Apr 26, 2021 (155)
3	gnomAD - Exomes	NC_000004.11 - 20728907	Jul 13, 2019 (153)
4	TopMed	NC_000004.12 - 20727284	Apr 26, 2021 (155)
5	ALFA	NC_000004.12 - 20727284	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
3539659, ss2734438506	NC_000004.11:20728906::G	NC_000004.12:20727283:GGGG:GGGGG	(self)
442826390, ss4605448834	NC_000004.12:20727283::G	NC_000004.12:20727283:GGGG:GGGGG	(self)
13124408449	NC_000004.12:20727283:GGGG:GGGGG	NC_000004.12:20727283:GGGG:GGGGG	(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 rs1491194692

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

rs1491194692