Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1490190116

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:75627792 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/264690, TOPMED)
G=0.000007 (1/140116, GnomAD)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LMO7 : Intron Variant
LMO7-AS1 : 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 14050 A=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 496 A=1.000 G=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 A=0.999996 G=0.000004
gnomAD - Genomes Global Study-wide 140116 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75868 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42012 A=1.00000 G=0.00000
gnomAD - Genomes American Sub 13642 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3312 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2148 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 14050 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
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 13 NC_000013.11:g.75627792A>G
GRCh37.p13 chr 13 NC_000013.10:g.76201928A>G
Gene: LMO7, LIM domain 7 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LMO7 transcript variant 1 NM_005358.5:c.225+4472A>G N/A Intron Variant
LMO7 transcript variant 3 NM_001306080.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 4 NM_001330583.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 5 NM_001366632.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 6 NM_001366633.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 7 NM_001366634.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 8 NM_001366636.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant 2 NM_015842.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X17 XM_047430323.1:c.-631+447…

XM_047430323.1:c.-631+4472A>G

 		N/A Intron Variant
LMO7 transcript variant X23 XM_047430329.1:c.-631+447…

XM_047430329.1:c.-631+4472A>G

 		N/A Intron Variant
LMO7 transcript variant X25 XM_011535095.3:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X14 XM_024449359.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X39 XM_024449363.2:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X1 XM_047430307.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X2 XM_047430308.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X3 XM_047430309.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X4 XM_047430310.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X5 XM_047430311.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X6 XM_047430312.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X7 XM_047430314.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X8 XM_047430315.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X9 XM_047430316.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X10 XM_047430317.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X11 XM_047430318.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X12 XM_047430319.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X13 XM_047430320.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X15 XM_047430321.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X16 XM_047430322.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X18 XM_047430324.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X19 XM_047430325.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X20 XM_047430326.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X21 XM_047430327.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X22 XM_047430328.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X24 XM_047430330.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X26 XM_047430331.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X27 XM_047430333.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X28 XM_047430334.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X29 XM_047430335.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X30 XM_047430336.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X31 XM_047430337.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X32 XM_047430338.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X33 XM_047430339.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X34 XM_047430340.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X35 XM_047430341.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X36 XM_047430342.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X37 XM_047430343.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X38 XM_047430344.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X40 XM_047430345.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X41 XM_047430346.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X42 XM_047430347.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X43 XM_047430348.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X44 XM_047430349.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X45 XM_047430350.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X46 XM_047430351.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X47 XM_047430352.1:c. N/A Genic Upstream Transcript Variant
LMO7 transcript variant X48 XM_047430353.1:c. N/A Genic Upstream Transcript Variant
Gene: LMO7-AS1, LMO7 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LMO7-AS1 transcript variant 1 NR_120410.1:n. N/A Intron Variant
LMO7-AS1 transcript variant 2 NR_120411.1:n. N/A Intron Variant
LMO7-AS1 transcript variant 3 NR_120412.1:n. N/A Intron 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 A= G
GRCh38.p14 chr 13 NC_000013.11:g.75627792= NC_000013.11:g.75627792A>G
GRCh37.p13 chr 13 NC_000013.10:g.76201928= NC_000013.10:g.76201928A>G
LMO7 transcript variant 1 NM_005358.5:c.225+4472= NM_005358.5:c.225+4472A>G
LMO7 transcript variant X1 XM_005266375.1:c.225+4472= XM_005266375.1:c.225+4472A>G
LMO7 transcript variant X2 XM_005266376.1:c.225+4472= XM_005266376.1:c.225+4472A>G
LMO7 transcript variant X3 XM_005266377.1:c.225+4472= XM_005266377.1:c.225+4472A>G
LMO7 transcript variant X4 XM_005266378.1:c.225+4472= XM_005266378.1:c.225+4472A>G
LMO7 transcript variant X5 XM_005266379.1:c.225+4472= XM_005266379.1:c.225+4472A>G
LMO7 transcript variant X6 XM_005266380.1:c.225+4472= XM_005266380.1:c.225+4472A>G
LMO7 transcript variant X8 XM_005266382.1:c.225+4472= XM_005266382.1:c.225+4472A>G
LMO7 transcript variant X11 XM_005266385.1:c.225+4472= XM_005266385.1:c.225+4472A>G
LMO7 transcript variant X12 XM_005266386.1:c.225+4472= XM_005266386.1:c.225+4472A>G
LMO7 transcript variant X14 XM_005266388.1:c.225+4472= XM_005266388.1:c.225+4472A>G
LMO7 transcript variant X16 XM_005266390.1:c.225+4472= XM_005266390.1:c.225+4472A>G
LMO7 transcript variant X19 XM_005266393.1:c.225+4472= XM_005266393.1:c.225+4472A>G
LMO7 transcript variant X20 XM_005266394.1:c.225+4472= XM_005266394.1:c.225+4472A>G
LMO7 transcript variant X21 XM_005266395.1:c.225+4472= XM_005266395.1:c.225+4472A>G
LMO7 transcript variant X24 XM_005266398.1:c.225+4472= XM_005266398.1:c.225+4472A>G
LMO7 transcript variant X17 XM_047430323.1:c.-631+4472= XM_047430323.1:c.-631+4472A>G
LMO7 transcript variant X23 XM_047430329.1:c.-631+4472= XM_047430329.1:c.-631+4472A>G
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 GNOMAD ss4268995063 Apr 26, 2021 (155)
2 TOPMED ss4952664957 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000013.11 - 75627792 Apr 26, 2021 (155)
4 TopMed NC_000013.11 - 75627792 Apr 26, 2021 (155)
5 ALFA NC_000013.11 - 75627792 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
435943810, 168210615, 6073238799, ss4268995063, ss4952664957 NC_000013.11:75627791:A:G NC_000013.11:75627791:A:G (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 rs1490190116

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