Name: rs1491466489
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.

rs1491466489

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:108165420-108165422 (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: Indel Insertion and Deletion
Frequency: delGG=0.427942 (59579/139222, GnomAD)
GGG=0.40887 (11553/28256, 14KJPN)
GGG=0.40710 (6823/16760, 8.3KJPN) (+ 4 more)
delGG=0.43277 (7068/16332, ALFA)
delGG=0.3987 (1786/4480, Estonian)
delGG=0.457 (96/210, Vietnamese)
delGG=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC25A24 : 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	16332	GGG=0.56723	G=0.43277	0.318883	0.184423	0.496694	1
European	Sub	12080	GGG=0.55919	G=0.44081	0.307119	0.188742	0.504139	2
African	Sub	2816	GGG=0.5938	G=0.4062	0.357955	0.170455	0.471591	0
African Others	Sub	108	GGG=0.602	G=0.398	0.388889	0.185185	0.425926	0
African American	Sub	2708	GGG=0.5934	G=0.4066	0.356721	0.169867	0.473412	0
Asian	Sub	108	GGG=0.343	G=0.657	0.074074	0.388889	0.537037	1
East Asian	Sub	84	GGG=0.35	G=0.65	0.071429	0.380952	0.547619	1
Other Asian	Sub	24	GGG=0.33	G=0.67	0.083333	0.416667	0.5	0
Latin American 1	Sub	146	GGG=0.568	G=0.432	0.342466	0.205479	0.452055	0
Latin American 2	Sub	610	GGG=0.630	G=0.370	0.386885	0.127869	0.485246	0
South Asian	Sub	94	GGG=0.59	G=0.41	0.340426	0.170213	0.489362	0
Other	Sub	478	GGG=0.582	G=0.418	0.343096	0.179916	0.476987	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
gnomAD - Genomes	Global	Study-wide	139222	GGG=0.572058	delGG=0.427942
gnomAD - Genomes	European	Sub	75370	GGG=0.55578	delGG=0.44422
gnomAD - Genomes	African	Sub	41756	GGG=0.60906	delGG=0.39094
gnomAD - Genomes	American	Sub	13556	GGG=0.60918	delGG=0.39082
gnomAD - Genomes	Ashkenazi Jewish	Sub	3294	GGG=0.4384	delGG=0.5616
gnomAD - Genomes	East Asian	Sub	3102	GGG=0.4697	delGG=0.5303
gnomAD - Genomes	Other	Sub	2144	GGG=0.5424	delGG=0.4576
14KJPN	JAPANESE	Study-wide	28256	GGG=0.40887	delGG=0.59113
8.3KJPN	JAPANESE	Study-wide	16760	GGG=0.40710	delGG=0.59290
Allele Frequency Aggregator	Total	Global	16332	GGG=0.56723	delGG=0.43277
Allele Frequency Aggregator	European	Sub	12080	GGG=0.55919	delGG=0.44081
Allele Frequency Aggregator	African	Sub	2816	GGG=0.5938	delGG=0.4062
Allele Frequency Aggregator	Latin American 2	Sub	610	GGG=0.630	delGG=0.370
Allele Frequency Aggregator	Other	Sub	478	GGG=0.582	delGG=0.418
Allele Frequency Aggregator	Latin American 1	Sub	146	GGG=0.568	delGG=0.432
Allele Frequency Aggregator	Asian	Sub	108	GGG=0.343	delGG=0.657
Allele Frequency Aggregator	South Asian	Sub	94	GGG=0.59	delGG=0.41
Genetic variation in the Estonian population	Estonian	Study-wide	4480	GGG=0.6013	delGG=0.3987
A Vietnamese Genetic Variation Database	Global	Study-wide	210	GGG=0.543	delGG=0.457
The Danish reference pan genome	Danish	Study-wide	40	GGG=0.55	delGG=0.45

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.108165421_108165422del
GRCh37.p13 chr 1	NC_000001.10:g.108708043_108708044del
SLC25A24 RefSeqGene	NG_032752.1:g.39938_39939del
GRCh38.p14 chr 1 novel patch HSCHR1_6_CTG3	NW_017852928.1:g.177589_177590insGG

Gene: SLC25A24, solute carrier family 25 member 24 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC25A24 transcript variant 1	NM_013386.5:c.399-4128_39… NM_013386.5:c.399-4128_399-4127del	N/A	Intron Variant
SLC25A24 transcript variant 2	NM_213651.3:c.342-4128_34… NM_213651.3:c.342-4128_342-4127del	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	GGG=	delGG
GRCh38.p14 chr 1	NC_000001.11:g.108165420_108165422=	NC_000001.11:g.108165421_108165422del
GRCh37.p13 chr 1	NC_000001.10:g.108708042_108708044=	NC_000001.10:g.108708043_108708044del
SLC25A24 RefSeqGene	NG_032752.1:g.39937_39939=	NG_032752.1:g.39938_39939del
GRCh38.p14 chr 1 novel patch HSCHR1_6_CTG3	NW_017852928.1:g.177589_177590insGG	NW_017852928.1:g.177589=
SLC25A24 transcript variant 1	NM_013386.4:c.399-4127=	NM_013386.4:c.399-4128_399-4127del
SLC25A24 transcript variant 1	NM_013386.5:c.399-4127=	NM_013386.5:c.399-4128_399-4127del
SLC25A24 transcript variant 2	NM_213651.2:c.342-4127=	NM_213651.2:c.342-4128_342-4127del
SLC25A24 transcript variant 2	NM_213651.3:c.342-4127=	NM_213651.3:c.342-4128_342-4127del

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#.

20 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	DDI	ss1536243364	Jan 10, 2018 (151)
2	EVA_GENOME_DK	ss1574004967	Jan 10, 2018 (151)
3	PADH-LAB_SPU	ss1751143348	Jan 10, 2018 (151)
4	JJLAB	ss2030342148	Jan 10, 2018 (151)
5	GNOMAD	ss2759329322	Jan 10, 2018 (151)
6	SWEGEN	ss2987405153	Jan 10, 2018 (151)
7	MCHAISSO	ss3063602873	Jan 10, 2018 (151)
8	MCHAISSO	ss3064418138	Jan 10, 2018 (151)
9	MCHAISSO	ss3064418139	Jan 10, 2018 (151)
10	URBANLAB	ss3646747664	Oct 11, 2018 (152)
11	EGCUT_WGS	ss3655494721	Jul 12, 2019 (153)
12	EVA_DECODE	ss3687490621	Jul 12, 2019 (153)
13	KHV_HUMAN_GENOMES	ss3799652372	Jul 12, 2019 (153)
14	EVA	ss3826359063	Apr 25, 2020 (154)
15	TOMMO_GENOMICS	ss5145588325	Apr 25, 2021 (155)
16	HUGCELL_USP	ss5444472572	Oct 12, 2022 (156)
17	SANFORD_IMAGENETICS	ss5626259659	Oct 12, 2022 (156)
18	TOMMO_GENOMICS	ss5670828422	Oct 12, 2022 (156)
19	YY_MCH	ss5800915245	Oct 12, 2022 (156)
20	EVA	ss5849060165	Oct 12, 2022 (156)
21	Genetic variation in the Estonian population	NC_000001.10 - 108708042	Oct 11, 2018 (152)
22	The Danish reference pan genome	NC_000001.10 - 108708042	Apr 25, 2020 (154)
23	gnomAD - Genomes	NC_000001.11 - 108165420	Apr 25, 2021 (155)
24	8.3KJPN	NC_000001.10 - 108708042	Apr 25, 2021 (155)
25	14KJPN	NC_000001.11 - 108165420	Oct 12, 2022 (156)
26	A Vietnamese Genetic Variation Database	NC_000001.10 - 108708042	Jul 12, 2019 (153)
27	ALFA	NC_000001.11 - 108165420	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
1232969, 165143, 3557632, 375248, ss1536243364, ss1574004967, ss1751143348, ss2030342148, ss2759329322, ss2987405153, ss3655494721, ss3826359063, ss5145588325, ss5626259659	NC_000001.10:108708041:GG:	NC_000001.11:108165419:GGG:G	(self)
22108948, 4665526, ss3063602873, ss3064418138, ss3064418139, ss3646747664, ss3687490621, ss3799652372, ss5444472572, ss5670828422, ss5800915245, ss5849060165	NC_000001.11:108165419:GG:	NC_000001.11:108165419:GGG:G	(self)
6733217368	NC_000001.11:108165419:GGG:G	NC_000001.11:108165419:GGG:G	(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 rs1491466489

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

rs1491466489