Name: rs1491478646
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.

rs1491478646

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:63177434-63177436 (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: delGA / dupGA / insGAGA / ins(GA)₄…
delGA / dupGA / insGAGA / ins(GA)₄ / ins(GA)₅ / ins(GA)₆ / ins(GA)₇ / ins(GA)₈
Variation Type: Indel Insertion and Deletion
Frequency: dupGA=0.000004 (1/264690, TOPMED)
delGA=0.00000 (0/11860, ALFA)
dupGA=0.00000 (0/11860, ALFA) (+ 4 more)
ins(GA)₅=0.00000 (0/11860, ALFA)
ins(GA)₆=0.00000 (0/11860, ALFA)
ins(GA)₇=0.00000 (0/11860, ALFA)
ins(GA)₆=0.005 (3/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC00466 : Intron Variant
LOC105378770 : 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	AGA=1.00000	A=0.00000, AGAGA=0.00000, AGAGAGAGAGAGA=0.00000, AGAGAGAGAGAGAGA=0.00000, AGAGAGAGAGAGAGAGA=0.00000	1.0	N/A
European	Sub	7618	AGA=1.0000	A=0.0000, AGAGA=0.0000, AGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGAGA=0.0000	1.0	N/A
African	Sub	2816	AGA=1.0000	A=0.0000, AGAGA=0.0000, AGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGAGA=0.0000	1.0	N/A
African Others	Sub	108	AGA=1.000	A=0.000, AGAGA=0.000, AGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGAGA=0.000	1.0	N/A
African American	Sub	2708	AGA=1.0000	A=0.0000, AGAGA=0.0000, AGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGA=0.0000, AGAGAGAGAGAGAGAGA=0.0000	1.0	N/A
Asian	Sub	108	AGA=1.000	A=0.000, AGAGA=0.000, AGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGAGA=0.000	1.0	N/A
East Asian	Sub	84	AGA=1.00	A=0.00, AGAGA=0.00, AGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGAGA=0.00	1.0	N/A
Other Asian	Sub	24	AGA=1.00	A=0.00, AGAGA=0.00, AGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGAGA=0.00	1.0	N/A
Latin American 1	Sub	146	AGA=1.000	A=0.000, AGAGA=0.000, AGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGAGA=0.000	1.0	N/A
Latin American 2	Sub	608	AGA=1.000	A=0.000, AGAGA=0.000, AGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGAGA=0.000	1.0	N/A
South Asian	Sub	94	AGA=1.00	A=0.00, AGAGA=0.00, AGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGA=0.00, AGAGAGAGAGAGAGAGA=0.00	1.0	N/A
Other	Sub	470	AGA=1.000	A=0.000, AGAGA=0.000, AGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGA=0.000, AGAGAGAGAGAGAGAGA=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	dupGA=0.000004
Allele Frequency Aggregator	Total	Global	11860	AGA=1.00000	delGA=0.00000, dupGA=0.00000, ins(GA)₅=0.00000, ins(GA)₆=0.00000, ins(GA)₇=0.00000
Allele Frequency Aggregator	European	Sub	7618	AGA=1.0000	delGA=0.0000, dupGA=0.0000, ins(GA)₅=0.0000, ins(GA)₆=0.0000, ins(GA)₇=0.0000
Allele Frequency Aggregator	African	Sub	2816	AGA=1.0000	delGA=0.0000, dupGA=0.0000, ins(GA)₅=0.0000, ins(GA)₆=0.0000, ins(GA)₇=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	608	AGA=1.000	delGA=0.000, dupGA=0.000, ins(GA)₅=0.000, ins(GA)₆=0.000, ins(GA)₇=0.000
Allele Frequency Aggregator	Other	Sub	470	AGA=1.000	delGA=0.000, dupGA=0.000, ins(GA)₅=0.000, ins(GA)₆=0.000, ins(GA)₇=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	AGA=1.000	delGA=0.000, dupGA=0.000, ins(GA)₅=0.000, ins(GA)₆=0.000, ins(GA)₇=0.000
Allele Frequency Aggregator	Asian	Sub	108	AGA=1.000	delGA=0.000, dupGA=0.000, ins(GA)₅=0.000, ins(GA)₆=0.000, ins(GA)₇=0.000
Allele Frequency Aggregator	South Asian	Sub	94	AGA=1.00	delGA=0.00, dupGA=0.00, ins(GA)₅=0.00, ins(GA)₆=0.00, ins(GA)₇=0.00
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	ins(GA)₆=0.005

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.63177435_63177436del
GRCh38.p14 chr 1	NC_000001.11:g.63177435_63177436dup
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[3]
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[5]
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[6]
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[7]
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[8]
GRCh38.p14 chr 1	NC_000001.11:g.63177435GA[9]
GRCh37.p13 chr 1	NC_000001.10:g.63643106_63643107del
GRCh37.p13 chr 1	NC_000001.10:g.63643106_63643107dup
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[3]
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[5]
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[6]
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[7]
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[8]
GRCh37.p13 chr 1	NC_000001.10:g.63643106GA[9]

Gene: LINC00466, long intergenic non-protein coding RNA 466 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00466 transcript	NR_038252.3:n.	N/A	Intron Variant

Gene: LOC105378770, uncharacterized LOC105378770 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378770 transcript	XR_947454.3: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	AGA=	delGA	dupGA	insGAGA	ins(GA)₄	ins(GA)₅	ins(GA)₆	ins(GA)₇	ins(GA)₈
GRCh38.p14 chr 1	NC_000001.11:g.63177434_63177436=	NC_000001.11:g.63177435_63177436del	NC_000001.11:g.63177435_63177436dup	NC_000001.11:g.63177435GA[3]	NC_000001.11:g.63177435GA[5]	NC_000001.11:g.63177435GA[6]	NC_000001.11:g.63177435GA[7]	NC_000001.11:g.63177435GA[8]	NC_000001.11:g.63177435GA[9]
GRCh37.p13 chr 1	NC_000001.10:g.63643105_63643107=	NC_000001.10:g.63643106_63643107del	NC_000001.10:g.63643106_63643107dup	NC_000001.10:g.63643106GA[3]	NC_000001.10:g.63643106GA[5]	NC_000001.10:g.63643106GA[6]	NC_000001.10:g.63643106GA[7]	NC_000001.10:g.63643106GA[8]	NC_000001.10:g.63643106GA[9]

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#.

21 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ACPOP	ss3727097607	Jul 12, 2019 (153)
2	EVA	ss3826201299	Apr 25, 2020 (154)
3	KOGIC	ss3944625093	Apr 25, 2020 (154)
4	KOGIC	ss3944625094	Apr 25, 2020 (154)
5	KOGIC	ss3944625096	Apr 25, 2020 (154)
6	GNOMAD	ss3994648571	Apr 25, 2021 (155)
7	GNOMAD	ss3994648572	Apr 25, 2021 (155)
8	GNOMAD	ss3994648573	Apr 25, 2021 (155)
9	GNOMAD	ss3994648574	Apr 25, 2021 (155)
10	GNOMAD	ss3994648575	Apr 25, 2021 (155)
11	GNOMAD	ss3994648576	Apr 25, 2021 (155)
12	GNOMAD	ss3994648577	Apr 25, 2021 (155)
13	TOPMED	ss4451763306	Apr 25, 2021 (155)
14	TOMMO_GENOMICS	ss5144207474	Apr 25, 2021 (155)
15	TOMMO_GENOMICS	ss5144207475	Apr 25, 2021 (155)
16	TOMMO_GENOMICS	ss5144207476	Apr 25, 2021 (155)
17	1000G_HIGH_COVERAGE	ss5242470324	Oct 12, 2022 (156)
18	HUGCELL_USP	ss5443512196	Oct 12, 2022 (156)
19	TOMMO_GENOMICS	ss5669052903	Oct 12, 2022 (156)
20	TOMMO_GENOMICS	ss5669052904	Oct 12, 2022 (156)
21	TOMMO_GENOMICS	ss5669052907	Oct 12, 2022 (156)
22	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
23	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
24	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
25	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
26	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
27	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
28	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13046755 (NC_000001.11:63177433::AG 2/112646) Row 13046756 (NC_000001.11:63177433::AGAG 7/112646) Row 13046757 (NC_000001.11:63177433::AGAGAGAG 9/112648)...	-	Apr 25, 2021 (155)
29	Korean Genome Project Submission ignored due to conflicting rows: Row 1003094 (NC_000001.11:63177433::AGAGAGAG 8/1832) Row 1003095 (NC_000001.11:63177433::AGAGAGAGAGAG 20/1832) Row 1003097 (NC_000001.11:63177433::AGAGAGAGAGAGAG 2/1832)	-	Apr 25, 2020 (154)
30	Korean Genome Project Submission ignored due to conflicting rows: Row 1003094 (NC_000001.11:63177433::AGAGAGAG 8/1832) Row 1003095 (NC_000001.11:63177433::AGAGAGAGAGAG 20/1832) Row 1003097 (NC_000001.11:63177433::AGAGAGAGAGAGAG 2/1832)	-	Apr 25, 2020 (154)
31	Korean Genome Project Submission ignored due to conflicting rows: Row 1003094 (NC_000001.11:63177433::AGAGAGAG 8/1832) Row 1003095 (NC_000001.11:63177433::AGAGAGAGAGAG 20/1832) Row 1003097 (NC_000001.11:63177433::AGAGAGAGAGAGAG 2/1832)	-	Apr 25, 2020 (154)
32	Northern Sweden	NC_000001.10 - 63643105	Jul 12, 2019 (153)
33	8.3KJPN Submission ignored due to conflicting rows: Row 2176781 (NC_000001.10:63643104::AGAGAGAGAGAG 405/16750) Row 2176782 (NC_000001.10:63643104::AGAGAGAGAG 56/16750) Row 2176783 (NC_000001.10:63643104::AGAGAGAGAGAGAGAG 16/16750)	-	Apr 25, 2021 (155)
34	8.3KJPN Submission ignored due to conflicting rows: Row 2176781 (NC_000001.10:63643104::AGAGAGAGAGAG 405/16750) Row 2176782 (NC_000001.10:63643104::AGAGAGAGAG 56/16750) Row 2176783 (NC_000001.10:63643104::AGAGAGAGAGAGAGAG 16/16750)	-	Apr 25, 2021 (155)
35	8.3KJPN Submission ignored due to conflicting rows: Row 2176781 (NC_000001.10:63643104::AGAGAGAGAGAG 405/16750) Row 2176782 (NC_000001.10:63643104::AGAGAGAGAG 56/16750) Row 2176783 (NC_000001.10:63643104::AGAGAGAGAGAGAGAG 16/16750)	-	Apr 25, 2021 (155)
36	14KJPN Submission ignored due to conflicting rows: Row 2890007 (NC_000001.11:63177433::AGAGAGAGAGAG 476/22410) Row 2890008 (NC_000001.11:63177433::AGAGAGAGAG 64/22410) Row 2890011 (NC_000001.11:63177433::AGAGAGAGAGAGAG 19/22410)	-	Oct 12, 2022 (156)
37	14KJPN Submission ignored due to conflicting rows: Row 2890007 (NC_000001.11:63177433::AGAGAGAGAGAG 476/22410) Row 2890008 (NC_000001.11:63177433::AGAGAGAGAG 64/22410) Row 2890011 (NC_000001.11:63177433::AGAGAGAGAGAGAG 19/22410)	-	Oct 12, 2022 (156)
38	14KJPN Submission ignored due to conflicting rows: Row 2890007 (NC_000001.11:63177433::AGAGAGAGAGAG 476/22410) Row 2890008 (NC_000001.11:63177433::AGAGAGAGAG 64/22410) Row 2890011 (NC_000001.11:63177433::AGAGAGAGAGAGAG 19/22410)	-	Oct 12, 2022 (156)
39	TopMed	NC_000001.11 - 63177434	Apr 25, 2021 (155)
40	ALFA	NC_000001.11 - 63177434	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
9709044875	NC_000001.11:63177433:AGA:A	NC_000001.11:63177433:AGA:A	(self)
15369641, ss3994648571, ss4451763306	NC_000001.11:63177433::AG	NC_000001.11:63177433:AGA:AGAGA	(self)
9709044875	NC_000001.11:63177433:AGA:AGAGA	NC_000001.11:63177433:AGA:AGAGA	(self)
ss3994648572	NC_000001.11:63177433::AGAG	NC_000001.11:63177433:AGA:AGAGAGA	(self)
ss3944625093, ss3994648573	NC_000001.11:63177433::AGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGA	(self)
ss5144207475	NC_000001.10:63643104::AGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGA	(self)
ss3994648574, ss5669052904	NC_000001.11:63177433::AGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGA	(self)
9709044875	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGA	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGA	(self)
382472, ss3727097607, ss3826201299, ss5144207474	NC_000001.10:63643104::AGAGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGA	(self)
ss3944625094, ss3994648575, ss5242470324, ss5443512196, ss5669052903	NC_000001.11:63177433::AGAGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGA	(self)
9709044875	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGA	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGA	(self)
ss3944625096, ss3994648576, ss5669052907	NC_000001.11:63177433::AGAGAGAGAGA… NC_000001.11:63177433::AGAGAGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGAGA	(self)
9709044875	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGAGA	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGAGA	(self)
ss5144207476	NC_000001.10:63643104::AGAGAGAGAGA… NC_000001.10:63643104::AGAGAGAGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGAGAGA	(self)
ss3994648577	NC_000001.11:63177433::AGAGAGAGAGA… NC_000001.11:63177433::AGAGAGAGAGAGAGAG	NC_000001.11:63177433:AGA:AGAGAGAG… NC_000001.11:63177433:AGA:AGAGAGAGAGAGAGAGAGA	(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 rs1491478646

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

rs1491478646