Name: rs535141730
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.

rs535141730

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:17143773 (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: dupA
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.002913 (771/264690, TOPMED)
dupA=0.002760 (387/140198, GnomAD)
dupA=0.00319 (59/18520, ALFA) (+ 6 more)
dupA=0.0009 (6/6404, 1000G_30x)
dupA=0.0008 (4/5008, 1000G)
dupA=0.0020 (9/4478, Estonian)
dupA=0.0029 (11/3854, ALSPAC)
dupA=0.0030 (11/3708, TWINSUK)
dupA=0.003 (2/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TRDMT1 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18520	A=0.99681	AA=0.00319
European	Sub	14152	A=0.99618	AA=0.00382
African	Sub	2898	A=0.9997	AA=0.0003
African Others	Sub	114	A=1.000	AA=0.000
African American	Sub	2784	A=0.9996	AA=0.0004
Asian	Sub	112	A=1.000	AA=0.000
East Asian	Sub	86	A=1.00	AA=0.00
Other Asian	Sub	26	A=1.00	AA=0.00
Latin American 1	Sub	146	A=1.000	AA=0.000
Latin American 2	Sub	610	A=0.997	AA=0.003
South Asian	Sub	98	A=1.00	AA=0.00
Other	Sub	504	A=0.996	AA=0.004

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	dupA=0.002913
gnomAD - Genomes	Global	Study-wide	140198	- No frequency provided	dupA=0.002760
gnomAD - Genomes	European	Sub	75928	- No frequency provided	dupA=0.00419
gnomAD - Genomes	African	Sub	42008	- No frequency provided	dupA=0.00079
gnomAD - Genomes	American	Sub	13652	- No frequency provided	dupA=0.00183
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	- No frequency provided	dupA=0.0021
gnomAD - Genomes	East Asian	Sub	3134	- No frequency provided	dupA=0.0000
gnomAD - Genomes	Other	Sub	2152	- No frequency provided	dupA=0.0019
Allele Frequency Aggregator	Total	Global	18520	A=0.99681	dupA=0.00319
Allele Frequency Aggregator	European	Sub	14152	A=0.99618	dupA=0.00382
Allele Frequency Aggregator	African	Sub	2898	A=0.9997	dupA=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.997	dupA=0.003
Allele Frequency Aggregator	Other	Sub	504	A=0.996	dupA=0.004
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	dupA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	dupA=0.00
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupA=0.0009
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupA=0.0000
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupA=0.0032
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupA=0.0000
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupA=0.0000
1000Genomes_30x	American	Sub	980	- No frequency provided	dupA=0.002
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupA=0.0008
1000Genomes	African	Sub	1322	- No frequency provided	dupA=0.0000
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupA=0.0000
1000Genomes	Europe	Sub	1006	- No frequency provided	dupA=0.0030
1000Genomes	South Asian	Sub	978	- No frequency provided	dupA=0.000
1000Genomes	American	Sub	694	- No frequency provided	dupA=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4478	- No frequency provided	dupA=0.0020
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupA=0.0029
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupA=0.0030
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupA=0.003

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 10	NC_000010.11:g.17143773dup
GRCh37.p13 chr 10	NC_000010.10:g.17185772dup

Gene: TRDMT1, tRNA aspartic acid methyltransferase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRDMT1 transcript variant a	NM_004412.7:c.*5267=	N/A	3 Prime UTR Variant
TRDMT1 transcript variant h	NM_001351219.2:c.*5267=	N/A	3 Prime UTR Variant
TRDMT1 transcript variant g	NM_001321007.2:c.*5267=	N/A	3 Prime UTR Variant
TRDMT1 transcript variant j	NM_001351221.2:c.*5267=	N/A	3 Prime UTR Variant
TRDMT1 transcript variant f	NM_001321006.2:c.*5267=	N/A	3 Prime UTR Variant
TRDMT1 transcript variant i	NM_001351220.2:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant k	NM_001351222.2:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant l	NM_001351223.2:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X2	XM_005252374.5:c.1076-457… XM_005252374.5:c.1076-4572dup	N/A	Intron Variant
TRDMT1 transcript variant X5	XM_047424695.1:c.1010-457… XM_047424695.1:c.1010-4572dup	N/A	Intron Variant
TRDMT1 transcript variant X8	XM_047424697.1:c.938-4572… XM_047424697.1:c.938-4572dup	N/A	Intron Variant
TRDMT1 transcript variant X6	XM_017015801.2:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X1	XM_024447855.2:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X3	XM_047424693.1:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X4	XM_047424694.1:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X7	XM_047424696.1:c.	N/A	Genic Downstream Transcript Variant
TRDMT1 transcript variant X9	XM_047424698.1:c.	N/A	Genic Downstream Transcript 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	A=	dupA
GRCh38.p14 chr 10	NC_000010.11:g.17143773=	NC_000010.11:g.17143773dup
GRCh37.p13 chr 10	NC_000010.10:g.17185772=	NC_000010.10:g.17185772dup
TRDMT1 transcript variant a	NM_004412.7:c.*5267=	NM_004412.7:c.*5267dup
TRDMT1 transcript variant a	NM_004412.6:c.*5267=	NM_004412.6:c.*5267dup
TRDMT1 transcript	NM_004412.5:c.*5267=	NM_004412.5:c.*5267dup
TRDMT1 transcript variant g	NM_001321007.2:c.*5267=	NM_001321007.2:c.*5267dup
TRDMT1 transcript variant g	NM_001321007.1:c.*5267=	NM_001321007.1:c.*5267dup
TRDMT1 transcript variant h	NM_001351219.2:c.*5267=	NM_001351219.2:c.*5267dup
TRDMT1 transcript variant h	NM_001351219.1:c.*5267=	NM_001351219.1:c.*5267dup
TRDMT1 transcript variant f	NM_001321006.2:c.*5267=	NM_001321006.2:c.*5267dup
TRDMT1 transcript variant f	NM_001321006.1:c.*5267=	NM_001321006.1:c.*5267dup
TRDMT1 transcript variant j	NM_001351221.2:c.*5267=	NM_001351221.2:c.*5267dup
TRDMT1 transcript variant j	NM_001351221.1:c.*5267=	NM_001351221.1:c.*5267dup
TRDMT1 transcript variant b	NM_176083.2:c.*5267=	NM_176083.2:c.*5267dup
TRDMT1 transcript variant c	NM_176081.2:c.*5267=	NM_176081.2:c.*5267dup
TRDMT1 transcript variant X3	XM_005252374.1:c.1076-4572=	XM_005252374.1:c.1076-4572dup
TRDMT1 transcript variant X2	XM_005252374.5:c.1076-4572=	XM_005252374.5:c.1076-4572dup
TRDMT1 transcript variant X5	XM_047424695.1:c.1010-4572=	XM_047424695.1:c.1010-4572dup
TRDMT1 transcript variant X8	XM_047424697.1:c.938-4572=	XM_047424697.1:c.938-4572dup

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#.

17 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1369183385	Aug 21, 2014 (142)
2	EVA_DECODE	ss1596903237	Apr 01, 2015 (144)
3	EVA_UK10K_ALSPAC	ss1706655560	Apr 01, 2015 (144)
4	EVA_UK10K_TWINSUK	ss1706655737	Apr 01, 2015 (144)
5	GNOMAD	ss2886065549	Nov 08, 2017 (151)
6	SWEGEN	ss3006020876	Nov 08, 2017 (151)
7	EGCUT_WGS	ss3673548818	Jul 13, 2019 (153)
8	EVA_DECODE	ss3689384961	Jul 13, 2019 (153)
9	ACPOP	ss3737108374	Jul 13, 2019 (153)
10	TOPMED	ss4844101743	Apr 26, 2021 (155)
11	1000G_HIGH_COVERAGE	ss5283100760	Oct 16, 2022 (156)
12	HUGCELL_USP	ss5478860558	Oct 16, 2022 (156)
13	1000G_HIGH_COVERAGE	ss5576568826	Oct 16, 2022 (156)
14	SANFORD_IMAGENETICS	ss5648780408	Oct 16, 2022 (156)
15	EVA	ss5824049212	Oct 16, 2022 (156)
16	EVA	ss5877942989	Oct 16, 2022 (156)
17	EVA	ss5940069563	Oct 16, 2022 (156)
18	1000Genomes	NC_000010.10 - 17185772	Oct 12, 2018 (152)
19	1000Genomes_30x	NC_000010.11 - 17143773	Oct 16, 2022 (156)
20	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 17185772	Oct 12, 2018 (152)
21	Genetic variation in the Estonian population	NC_000010.10 - 17185772	Oct 12, 2018 (152)
22	gnomAD - Genomes	NC_000010.11 - 17143773	Apr 26, 2021 (155)
23	Northern Sweden	NC_000010.10 - 17185772	Jul 13, 2019 (153)
24	TopMed	NC_000010.11 - 17143773	Apr 26, 2021 (155)
25	UK 10K study - Twins	NC_000010.10 - 17185772	Oct 12, 2018 (152)
26	ALFA	NC_000010.11 - 17143773	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
ss1596903237	NC_000010.9:17225777::A	NC_000010.11:17143772:A:AA	(self)
48833756, 27137247, 19287066, 10393239, 27137247, ss1369183385, ss1706655560, ss1706655737, ss2886065549, ss3006020876, ss3673548818, ss3737108374, ss5648780408, ss5824049212, ss5940069563	NC_000010.10:17185771::A	NC_000010.11:17143772:A:AA	(self)
64094761, 344855747, 59647398, ss3689384961, ss4844101743, ss5283100760, ss5478860558, ss5576568826, ss5877942989	NC_000010.11:17143772::A	NC_000010.11:17143772:A:AA	(self)
14367616162	NC_000010.11:17143772:A:AA	NC_000010.11:17143772:A:AA	(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 rs535141730

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

rs535141730