Name: rs1491268582
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.

rs1491268582

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:128899523-128899524 (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: delGG
Variation Type: Deletion
Frequency: delGG=0.00208 (184/88494, GnomAD)
delGG=0.00046 (13/28172, 14KJPN)
delGG=0.00066 (11/16708, 8.3KJPN) (+ 1 more)
delGG=0.00000 (0/11810, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ACAD9 : 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	11810	GG=1.00000	=0.00000	1.0	N/A
European	Sub	7616	GG=1.0000	=0.0000	1.0	N/A
African	Sub	2772	GG=1.0000	=0.0000	1.0	N/A
African Others	Sub	108	GG=1.000	=0.000	1.0	N/A
African American	Sub	2664	GG=1.0000	=0.0000	1.0	N/A
Asian	Sub	106	GG=1.000	=0.000	1.0	N/A
East Asian	Sub	82	GG=1.00	=0.00	1.0	N/A
Other Asian	Sub	24	GG=1.00	=0.00	1.0	N/A
Latin American 1	Sub	146	GG=1.000	=0.000	1.0	N/A
Latin American 2	Sub	610	GG=1.000	=0.000	1.0	N/A
South Asian	Sub	94	GG=1.00	=0.00	1.0	N/A
Other	Sub	466	GG=1.000	=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	88494	GG=0.99792	delGG=0.00208
gnomAD - Genomes	European	Sub	54072	GG=0.99970	delGG=0.00030
gnomAD - Genomes	African	Sub	20534	GG=0.99235	delGG=0.00765
gnomAD - Genomes	American	Sub	8752	GG=0.9995	delGG=0.0005
gnomAD - Genomes	Ashkenazi Jewish	Sub	2310	GG=1.0000	delGG=0.0000
gnomAD - Genomes	East Asian	Sub	1496	GG=0.9973	delGG=0.0027
gnomAD - Genomes	Other	Sub	1330	GG=0.9977	delGG=0.0023
14KJPN	JAPANESE	Study-wide	28172	GG=0.99954	delGG=0.00046
8.3KJPN	JAPANESE	Study-wide	16708	GG=0.99934	delGG=0.00066
Allele Frequency Aggregator	Total	Global	11810	GG=1.00000	delGG=0.00000
Allele Frequency Aggregator	European	Sub	7616	GG=1.0000	delGG=0.0000
Allele Frequency Aggregator	African	Sub	2772	GG=1.0000	delGG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	GG=1.000	delGG=0.000
Allele Frequency Aggregator	Other	Sub	466	GG=1.000	delGG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	GG=1.000	delGG=0.000
Allele Frequency Aggregator	Asian	Sub	106	GG=1.000	delGG=0.000
Allele Frequency Aggregator	South Asian	Sub	94	GG=1.00	delGG=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.128899523_128899524del
GRCh37.p13 chr 3	NC_000003.11:g.128618366_128618367del
ACAD9 RefSeqGene	NG_017064.1:g.25034_25035del

Gene: ACAD9, acyl-CoA dehydrogenase family member 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ACAD9 transcript variant 1	NM_014049.5:c.808+62_808+… NM_014049.5:c.808+62_808+63del	N/A	Intron Variant
ACAD9 transcript variant 2	NR_033426.2:n.	N/A	Intron Variant
ACAD9 transcript variant X1	XM_024453484.2:c.439+62_4… XM_024453484.2:c.439+62_439+63del	N/A	Intron Variant
ACAD9 transcript variant X1	XM_024453485.2:c.439+62_4… XM_024453485.2:c.439+62_439+63del	N/A	Intron Variant
ACAD9 transcript variant X2	XR_427367.4: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	GG=	delGG
GRCh38.p14 chr 3	NC_000003.12:g.128899523_128899524=	NC_000003.12:g.128899523_128899524del
GRCh37.p13 chr 3	NC_000003.11:g.128618366_128618367=	NC_000003.11:g.128618366_128618367del
ACAD9 RefSeqGene	NG_017064.1:g.25034_25035=	NG_017064.1:g.25034_25035del
ACAD9 transcript variant 1	NM_014049.4:c.808+62=	NM_014049.4:c.808+62_808+63del
ACAD9 transcript variant 1	NM_014049.5:c.808+62=	NM_014049.5:c.808+62_808+63del
ACAD9 transcript variant X1	XM_024453484.2:c.439+62=	XM_024453484.2:c.439+62_439+63del
ACAD9 transcript variant X1	XM_024453485.2:c.439+62=	XM_024453485.2:c.439+62_439+63del

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#.

5 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_DECODE	ss3710259857	Jul 13, 2019 (153)
2	EVA	ss3986253937	Apr 26, 2021 (155)
3	GNOMAD	ss4080539796	Apr 26, 2021 (155)
4	TOMMO_GENOMICS	ss5161516506	Apr 26, 2021 (155)
5	TOMMO_GENOMICS	ss5694372085	Oct 12, 2022 (156)
6	gnomAD - Genomes	NC_000003.12 - 128899523	Apr 26, 2021 (155)
7	8.3KJPN	NC_000003.11 - 128618366	Apr 26, 2021 (155)
8	14KJPN	NC_000003.12 - 128899523	Oct 12, 2022 (156)
9	ALFA	NC_000003.12 - 128899523	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
19485813, ss3986253937, ss5161516506	NC_000003.11:128618365:GG:	NC_000003.12:128899522:GG:	(self)
123362966, 28209189, 6741774898, ss3710259857, ss4080539796, ss5694372085	NC_000003.12:128899522:GG:	NC_000003.12:128899522:GG:	(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 rs1491268582

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

rs1491268582