Name: rs1486242991
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.

rs1486242991

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:155614705-155614710 (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: delGAT
Variation Type: Indel Insertion and Deletion
Frequency: delGAT=0.000011 (3/264690, TOPMED)
delGAT=0.000014 (2/140198, GnomAD)
delGAT=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MSTO1 : Non Coding Transcript 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	14050	GATGAT=1.00000	GAT=0.00000	1.0	N/A
European	Sub	9690	GATGAT=1.0000	GAT=0.0000	1.0	N/A
African	Sub	2898	GATGAT=1.0000	GAT=0.0000	1.0	N/A
African Others	Sub	114	GATGAT=1.000	GAT=0.000	1.0	N/A
African American	Sub	2784	GATGAT=1.0000	GAT=0.0000	1.0	N/A
Asian	Sub	112	GATGAT=1.000	GAT=0.000	1.0	N/A
East Asian	Sub	86	GATGAT=1.00	GAT=0.00	1.0	N/A
Other Asian	Sub	26	GATGAT=1.00	GAT=0.00	1.0	N/A
Latin American 1	Sub	146	GATGAT=1.000	GAT=0.000	1.0	N/A
Latin American 2	Sub	610	GATGAT=1.000	GAT=0.000	1.0	N/A
South Asian	Sub	98	GATGAT=1.00	GAT=0.00	1.0	N/A
Other	Sub	496	GATGAT=1.000	GAT=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	(GAT)₂=0.999989	delGAT=0.000011
gnomAD - Genomes	Global	Study-wide	140198	(GAT)₂=0.999986	delGAT=0.000014
gnomAD - Genomes	European	Sub	75934	(GAT)₂=1.00000	delGAT=0.00000
gnomAD - Genomes	African	Sub	42012	(GAT)₂=0.99995	delGAT=0.00005
gnomAD - Genomes	American	Sub	13648	(GAT)₂=1.00000	delGAT=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	(GAT)₂=1.0000	delGAT=0.0000
gnomAD - Genomes	East Asian	Sub	3130	(GAT)₂=1.0000	delGAT=0.0000
gnomAD - Genomes	Other	Sub	2152	(GAT)₂=1.0000	delGAT=0.0000
Allele Frequency Aggregator	Total	Global	14050	(GAT)₂=1.00000	delGAT=0.00000
Allele Frequency Aggregator	European	Sub	9690	(GAT)₂=1.0000	delGAT=0.0000
Allele Frequency Aggregator	African	Sub	2898	(GAT)₂=1.0000	delGAT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(GAT)₂=1.000	delGAT=0.000
Allele Frequency Aggregator	Other	Sub	496	(GAT)₂=1.000	delGAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(GAT)₂=1.000	delGAT=0.000
Allele Frequency Aggregator	Asian	Sub	112	(GAT)₂=1.000	delGAT=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(GAT)₂=1.00	delGAT=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 1	NC_000001.11:g.155614705GAT[1]
GRCh37.p13 chr 1	NC_000001.10:g.155584496GAT[1]

Gene: MSTO1, misato mitochondrial distribution and morphology regulator 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MSTO1 transcript variant 2	NM_001256532.1:c.432_43… NM_001256532.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 3	NM_001256533.1:c.432_43… NM_001256533.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 17	NM_001350781.1:c.432_43… NM_001350781.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 16	NM_001350780.1:c.432_43… NM_001350780.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 11	NM_001350775.1:c.505_51… NM_001350775.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 14	NM_001350778.1:c.432_43… NM_001350778.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 19	NM_001350783.1:c.432_43… NM_001350783.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 15	NM_001350779.1:c.432_43… NM_001350779.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 12	NM_001350776.1:c.432_43… NM_001350776.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 21	NM_001350785.1:c.432_43… NM_001350785.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 13	NM_001350777.1:c.432_43… NM_001350777.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 18	NM_001350782.1:c.432_43… NM_001350782.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 25	NM_001350789.1:c.505_51… NM_001350789.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 8	NM_001350772.1:c.432_43… NM_001350772.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 9	NM_001350773.1:c.505_51… NM_001350773.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 10	NM_001350774.1:c.505_51… NM_001350774.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 22	NM_001350786.1:c.505_51… NM_001350786.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 20	NM_001350784.1:c.432_43… NM_001350784.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 23	NM_001350787.1:c.432_43… NM_001350787.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 24	NM_001350788.1:c.505_51… NM_001350788.1:c.505_510=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 1	NM_018116.4:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant 4	NR_046292.1:n.2313GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant 5	NR_046293.1:n.2255GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant 6	NR_046294.1:n.2247GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant 7	NR_046295.1:n.2148GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant 27	NR_146908.1:n.2262GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant 26	NR_146907.1:n.2181GAT[1]	N/A	Non Coding Transcript Variant
MSTO1 transcript variant X1	XM_047424007.1:c.432_43… XM_047424007.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant X2	XM_047424008.1:c.432_43… XM_047424008.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant X3	XM_047424011.1:c.432_43… XM_047424011.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant X4	XM_047424021.1:c.432_43… XM_047424021.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant X5	XM_047424030.1:c.432_43… XM_047424030.1:c.432_437=	N/A	3 Prime UTR Variant
MSTO1 transcript variant X6	XM_047424040.1:c.432_43… XM_047424040.1:c.432_437=	N/A	3 Prime UTR 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	(GAT)₂=	delGAT
GRCh38.p14 chr 1	NC_000001.11:g.155614705_155614710=	NC_000001.11:g.155614705GAT[1]
GRCh37.p13 chr 1	NC_000001.10:g.155584496_155584501=	NC_000001.10:g.155584496GAT[1]
MSTO1 transcript variant 1	NM_018116.4:c.432_437=	NM_018116.4:c.*432GAT[1]
MSTO1 transcript variant 1	NM_018116.3:c.432_437=	NM_018116.3:c.*432GAT[1]
MSTO1 transcript variant X1	XM_047424007.1:c.432_437=	XM_047424007.1:c.*432GAT[1]
MSTO1 transcript variant X4	XM_047424021.1:c.432_437=	XM_047424021.1:c.*432GAT[1]
MSTO1 transcript variant 17	NM_001350781.1:c.432_437=	NM_001350781.1:c.*432GAT[1]
MSTO1 transcript variant X3	XM_047424011.1:c.432_437=	XM_047424011.1:c.*432GAT[1]
MSTO1 transcript variant X2	XM_047424008.1:c.432_437=	XM_047424008.1:c.*432GAT[1]
MSTO1 transcript variant 21	NM_001350785.1:c.432_437=	NM_001350785.1:c.*432GAT[1]
MSTO1 transcript variant X5	XM_047424030.1:c.432_437=	XM_047424030.1:c.*432GAT[1]
MSTO1 transcript variant 25	NM_001350789.1:c.505_510=	NM_001350789.1:c.*505GAT[1]
MSTO1 transcript variant 16	NM_001350780.1:c.432_437=	NM_001350780.1:c.*432GAT[1]
MSTO1 transcript variant 12	NM_001350776.1:c.432_437=	NM_001350776.1:c.*432GAT[1]
MSTO1 transcript variant 22	NM_001350786.1:c.505_510=	NM_001350786.1:c.*505GAT[1]
MSTO1 transcript variant 4	NR_046292.1:n.2313_2318=	NR_046292.1:n.2313GAT[1]
MSTO1 transcript variant 24	NM_001350788.1:c.505_510=	NM_001350788.1:c.*505GAT[1]
MSTO1 transcript variant 14	NM_001350778.1:c.432_437=	NM_001350778.1:c.*432GAT[1]
MSTO1 transcript variant 20	NM_001350784.1:c.432_437=	NM_001350784.1:c.*432GAT[1]
MSTO1 transcript variant 18	NM_001350782.1:c.432_437=	NM_001350782.1:c.*432GAT[1]
MSTO1 transcript variant 19	NM_001350783.1:c.432_437=	NM_001350783.1:c.*432GAT[1]
MSTO1 transcript variant 27	NR_146908.1:n.2262_2267=	NR_146908.1:n.2262GAT[1]
MSTO1 transcript variant 9	NM_001350773.1:c.505_510=	NM_001350773.1:c.*505GAT[1]
MSTO1 transcript variant 10	NM_001350774.1:c.505_510=	NM_001350774.1:c.*505GAT[1]
MSTO1 transcript variant 5	NR_046293.1:n.2255_2260=	NR_046293.1:n.2255GAT[1]
MSTO1 transcript variant 15	NM_001350779.1:c.432_437=	NM_001350779.1:c.*432GAT[1]
MSTO1 transcript variant 23	NM_001350787.1:c.432_437=	NM_001350787.1:c.*432GAT[1]
MSTO1 transcript variant 13	NM_001350777.1:c.432_437=	NM_001350777.1:c.*432GAT[1]
MSTO1 transcript variant 11	NM_001350775.1:c.505_510=	NM_001350775.1:c.*505GAT[1]
MSTO1 transcript variant 6	NR_046294.1:n.2247_2252=	NR_046294.1:n.2247GAT[1]
MSTO1 transcript variant 2	NM_001256532.1:c.432_437=	NM_001256532.1:c.*432GAT[1]
MSTO1 transcript variant 8	NM_001350772.1:c.432_437=	NM_001350772.1:c.*432GAT[1]
MSTO1 transcript variant 3	NM_001256533.1:c.432_437=	NM_001256533.1:c.*432GAT[1]
MSTO1 transcript variant 26	NR_146907.1:n.2181_2186=	NR_146907.1:n.2181GAT[1]
MSTO1 transcript variant 7	NR_046295.1:n.2148_2153=	NR_046295.1:n.2148GAT[1]
MSTO1 transcript variant X6	XM_047424040.1:c.432_437=	XM_047424040.1:c.*432GAT[1]

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	ss4003861463	Apr 25, 2021 (155)
2	TOPMED	ss4468550649	Apr 25, 2021 (155)
3	gnomAD - Genomes	NC_000001.11 - 155614705	Apr 25, 2021 (155)
4	TopMed	NC_000001.11 - 155614705	Apr 25, 2021 (155)
5	ALFA	NC_000001.11 - 155614705	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
27259084, 32156984, ss4003861463, ss4468550649	NC_000001.11:155614704:GAT:	NC_000001.11:155614704:GATGAT:GAT	(self)
5547036500	NC_000001.11:155614704:GATGAT:GAT	NC_000001.11:155614704:GATGAT:GAT	(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 rs1486242991

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

rs1486242991