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dbSNP Short Genetic Variations

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.

rs1489151172

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:87196144 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.00043 (7/16332, ALFA)
A=0.0016 (7/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DMTF1 : Non Coding Transcript Variant
TMEM243 : 500B Downstream Variant
LOC105375384 : 2KB Upstream 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 G=0.99957 A=0.00043 0.999143 0.0 0.000857 0
European Sub 12080 G=0.99942 A=0.00058 0.998841 0.0 0.001159 0
African Sub 2816 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 478 G=1.000 A=0.000 1.0 0.0 0.0 N/A


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999996 A=0.000004
Allele Frequency Aggregator Total Global 16332 G=0.99957 A=0.00043
Allele Frequency Aggregator European Sub 12080 G=0.99942 A=0.00058
Allele Frequency Aggregator African Sub 2816 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 478 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9984 A=0.0016
Help

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 7 NC_000007.14:g.87196144G>A
GRCh37.p13 chr 7 NC_000007.13:g.86825460G>A
DMTF1 RefSeqGene NG_029536.1:g.48784G>A
Gene: DMTF1, cyclin D binding myb like transcription factor 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DMTF1 transcript variant 2 NM_001142327.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant 3 NM_001142326.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant 1 NM_021145.4:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant 4 NR_024549.2:n.3732G>A N/A Non Coding Transcript Variant
DMTF1 transcript variant 5 NR_024550.2:n.3693G>A N/A Non Coding Transcript Variant
DMTF1 transcript variant X1 XM_011516737.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X33 XM_017012868.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X43 XM_047421099.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X2 XM_047421100.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X3 XM_024447016.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X4 XM_024447020.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X14 XM_024447019.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X5 XM_024447018.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X6 XM_024447017.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X7 XM_047421101.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X8 XM_047421102.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X9 XM_024447022.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X16 XM_024447021.2:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X44 XM_047421103.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X17 XM_047421104.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X18 XM_047421105.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X10 XM_047421106.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X11 XM_047421107.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X12 XM_047421108.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X45 XM_047421109.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X46 XM_047421110.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X13 XM_047421111.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X15 XM_047421112.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X47 XM_047421113.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X19 XM_011516739.4:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X20 XM_047421114.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X21 XM_047421115.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X22 XM_047421116.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X23 XM_047421117.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X24 XM_047421118.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X25 XM_047421119.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X26 XM_047421120.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X27 XM_047421121.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X28 XM_047421122.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X29 XM_047421123.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X30 XM_047421124.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X31 XM_047421125.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X32 XM_047421126.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X37 XM_047421127.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X34 XM_047421128.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X48 XM_047421129.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X35 XM_047421130.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X36 XM_047421131.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X38 XM_047421132.1:c.*1004= N/A 3 Prime UTR Variant
DMTF1 transcript variant X39 XM_017012870.3:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X40 XM_047421133.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X41 XM_047421134.1:c.*1015= N/A 3 Prime UTR Variant
DMTF1 transcript variant X42 XM_047421135.1:c.*1015= N/A 3 Prime UTR Variant
Gene: TMEM243, transmembrane protein 243 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TMEM243 transcript variant 2 NM_001329472.1:c. N/A Downstream Transcript Variant
TMEM243 transcript variant 3 NM_001329473.2:c. N/A Downstream Transcript Variant
TMEM243 transcript variant 4 NM_001329474.2:c. N/A Downstream Transcript Variant
TMEM243 transcript variant 5 NM_001329475.2:c. N/A Downstream Transcript Variant
TMEM243 transcript variant 1 NM_024315.4:c. N/A Downstream Transcript Variant
TMEM243 transcript variant 6 NR_138030.2:n. N/A Downstream Transcript Variant
TMEM243 transcript variant X1 XM_005250586.4:c. N/A N/A
TMEM243 transcript variant X2 XM_005250587.5:c. N/A N/A
TMEM243 transcript variant X2 XM_005250588.4:c. N/A N/A
Gene: LOC105375384, uncharacterized LOC105375384 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105375384 transcript XR_927722.3:n. N/A Upstream Transcript Variant
Help

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
Help

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 G= A
GRCh38.p14 chr 7 NC_000007.14:g.87196144= NC_000007.14:g.87196144G>A
GRCh37.p13 chr 7 NC_000007.13:g.86825460= NC_000007.13:g.86825460G>A
DMTF1 RefSeqGene NG_029536.1:g.48784= NG_029536.1:g.48784G>A
DMTF1 transcript variant 1 NM_021145.4:c.*1004= NM_021145.4:c.*1004G>A
DMTF1 transcript variant 1 NM_021145.3:c.*1004= NM_021145.3:c.*1004G>A
DMTF1 transcript variant 4 NR_024549.2:n.3732= NR_024549.2:n.3732G>A
DMTF1 transcript variant 4 NR_024549.1:n.3824= NR_024549.1:n.3824G>A
DMTF1 transcript variant 5 NR_024550.2:n.3693= NR_024550.2:n.3693G>A
DMTF1 transcript variant 5 NR_024550.1:n.3785= NR_024550.1:n.3785G>A
DMTF1 transcript variant 2 NM_001142327.2:c.*1004= NM_001142327.2:c.*1004G>A
DMTF1 transcript variant 2 NM_001142327.1:c.*1004= NM_001142327.1:c.*1004G>A
DMTF1 transcript variant 3 NM_001142326.2:c.*1004= NM_001142326.2:c.*1004G>A
DMTF1 transcript variant 3 NM_001142326.1:c.*1004= NM_001142326.1:c.*1004G>A
DMTF1 transcript variant X19 XM_011516739.4:c.*1004= XM_011516739.4:c.*1004G>A
DMTF1 transcript variant X17 XM_011516739.3:c.*1004= XM_011516739.3:c.*1004G>A
DMTF1 transcript variant X5 XM_011516739.2:c.*1004= XM_011516739.2:c.*1004G>A
DMTF1 transcript variant X11 XM_011516739.1:c.*1004= XM_011516739.1:c.*1004G>A
DMTF1 transcript variant X39 XM_017012870.3:c.*1015= XM_017012870.3:c.*1015G>A
DMTF1 transcript variant X24 XM_017012870.2:c.*1015= XM_017012870.2:c.*1015G>A
DMTF1 transcript variant X9 XM_017012870.1:c.*1015= XM_017012870.1:c.*1015G>A
DMTF1 transcript variant X6 XM_024447017.2:c.*1004= XM_024447017.2:c.*1004G>A
DMTF1 transcript variant X9 XM_024447017.1:c.*1004= XM_024447017.1:c.*1004G>A
DMTF1 transcript variant X14 XM_024447019.2:c.*1004= XM_024447019.2:c.*1004G>A
DMTF1 transcript variant X12 XM_024447019.1:c.*1004= XM_024447019.1:c.*1004G>A
DMTF1 transcript variant X16 XM_024447021.2:c.*1004= XM_024447021.2:c.*1004G>A
DMTF1 transcript variant X14 XM_024447021.1:c.*1004= XM_024447021.1:c.*1004G>A
DMTF1 transcript variant X5 XM_024447018.2:c.*1004= XM_024447018.2:c.*1004G>A
DMTF1 transcript variant X10 XM_024447018.1:c.*1004= XM_024447018.1:c.*1004G>A
DMTF1 transcript variant X9 XM_024447022.2:c.*1004= XM_024447022.2:c.*1004G>A
DMTF1 transcript variant X15 XM_024447022.1:c.*1004= XM_024447022.1:c.*1004G>A
DMTF1 transcript variant X3 XM_024447016.2:c.*1004= XM_024447016.2:c.*1004G>A
DMTF1 transcript variant X8 XM_024447016.1:c.*1004= XM_024447016.1:c.*1004G>A
DMTF1 transcript variant X4 XM_024447020.2:c.*1004= XM_024447020.2:c.*1004G>A
DMTF1 transcript variant X13 XM_024447020.1:c.*1004= XM_024447020.1:c.*1004G>A
DMTF1 transcript variant X43 XM_047421099.1:c.*1004= XM_047421099.1:c.*1004G>A
DMTF1 transcript variant X10 XM_047421106.1:c.*1004= XM_047421106.1:c.*1004G>A
DMTF1 transcript variant X12 XM_047421108.1:c.*1004= XM_047421108.1:c.*1004G>A
DMTF1 transcript variant X11 XM_047421107.1:c.*1004= XM_047421107.1:c.*1004G>A
DMTF1 transcript variant X15 XM_047421112.1:c.*1004= XM_047421112.1:c.*1004G>A
DMTF1 transcript variant X13 XM_047421111.1:c.*1004= XM_047421111.1:c.*1004G>A
DMTF1 transcript variant X45 XM_047421109.1:c.*1004= XM_047421109.1:c.*1004G>A
DMTF1 transcript variant X8 XM_047421102.1:c.*1004= XM_047421102.1:c.*1004G>A
DMTF1 transcript variant X46 XM_047421110.1:c.*1004= XM_047421110.1:c.*1004G>A
DMTF1 transcript variant X29 XM_047421123.1:c.*1015= XM_047421123.1:c.*1015G>A
DMTF1 transcript variant X30 XM_047421124.1:c.*1015= XM_047421124.1:c.*1015G>A
DMTF1 transcript variant X47 XM_047421113.1:c.*1004= XM_047421113.1:c.*1004G>A
DMTF1 transcript variant X48 XM_047421129.1:c.*1015= XM_047421129.1:c.*1015G>A
DMTF1 transcript variant X20 XM_047421114.1:c.*1004= XM_047421114.1:c.*1004G>A
DMTF1 transcript variant X21 XM_047421115.1:c.*1004= XM_047421115.1:c.*1004G>A
DMTF1 transcript variant X7 XM_047421101.1:c.*1004= XM_047421101.1:c.*1004G>A
DMTF1 transcript variant X2 XM_047421100.1:c.*1004= XM_047421100.1:c.*1004G>A
DMTF1 transcript variant X17 XM_047421104.1:c.*1004= XM_047421104.1:c.*1004G>A
DMTF1 transcript variant X18 XM_047421105.1:c.*1004= XM_047421105.1:c.*1004G>A
DMTF1 transcript variant X31 XM_047421125.1:c.*1015= XM_047421125.1:c.*1015G>A
DMTF1 transcript variant X37 XM_047421127.1:c.*1015= XM_047421127.1:c.*1015G>A
DMTF1 transcript variant X26 XM_047421120.1:c.*1004= XM_047421120.1:c.*1004G>A
DMTF1 transcript variant X27 XM_047421121.1:c.*1004= XM_047421121.1:c.*1004G>A
DMTF1 transcript variant X22 XM_047421116.1:c.*1004= XM_047421116.1:c.*1004G>A
DMTF1 transcript variant X35 XM_047421130.1:c.*1015= XM_047421130.1:c.*1015G>A
DMTF1 transcript variant X44 XM_047421103.1:c.*1004= XM_047421103.1:c.*1004G>A
DMTF1 transcript variant X36 XM_047421131.1:c.*1015= XM_047421131.1:c.*1015G>A
DMTF1 transcript variant X1 XM_011516737.1:c.*1004= XM_011516737.1:c.*1004G>A
DMTF1 transcript variant X25 XM_047421119.1:c.*1004= XM_047421119.1:c.*1004G>A
DMTF1 transcript variant X32 XM_047421126.1:c.*1015= XM_047421126.1:c.*1015G>A
DMTF1 transcript variant X24 XM_047421118.1:c.*1004= XM_047421118.1:c.*1004G>A
DMTF1 transcript variant X33 XM_017012868.1:c.*1015= XM_017012868.1:c.*1015G>A
DMTF1 transcript variant X23 XM_047421117.1:c.*1004= XM_047421117.1:c.*1004G>A
DMTF1 transcript variant X40 XM_047421133.1:c.*1015= XM_047421133.1:c.*1015G>A
DMTF1 transcript variant X34 XM_047421128.1:c.*1015= XM_047421128.1:c.*1015G>A
DMTF1 transcript variant X41 XM_047421134.1:c.*1015= XM_047421134.1:c.*1015G>A
DMTF1 transcript variant X28 XM_047421122.1:c.*1015= XM_047421122.1:c.*1015G>A
DMTF1 transcript variant X38 XM_047421132.1:c.*1004= XM_047421132.1:c.*1004G>A
DMTF1 transcript variant X42 XM_047421135.1:c.*1015= XM_047421135.1:c.*1015G>A
Help

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 EGCUT_WGS ss3669327340 Jul 13, 2019 (153)
2 TOPMED ss4753559166 Apr 26, 2021 (155)
3 Genetic variation in the Estonian population NC_000007.13 - 86825460 Oct 12, 2018 (152)
4 TopMed NC_000007.14 - 87196144 Apr 26, 2021 (155)
5 ALFA NC_000007.14 - 87196144 Apr 26, 2021 (155)
Help

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
15065588, ss3669327340 NC_000007.13:86825459:G:A NC_000007.14:87196143:G:A (self)
590936725, 6005924554, ss4753559166 NC_000007.14:87196143:G:A NC_000007.14:87196143:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1489151172

Help

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.

Software version is: 2.0.1.post820+afb47a3d