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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.

rs1391662275

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:118531051 (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=0.000008 (2/264690, TOPMED)
A=0.000007 (1/140200, GnomAD)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTC36-AS1 : Non Coding Transcript Variant
TMEM25 : 2KB Upstream Variant
TTC36 : 500B Downstream 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 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 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 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 496 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=0.999992 A=0.000008
gnomAD - Genomes Global Study-wide 140200 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75896 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42044 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13658 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 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 496 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 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=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 11 NC_000011.10:g.118531051G>A
GRCh37.p13 chr 11 NC_000011.9:g.118401766G>A
GRCh37.p13 chr 11 fix patch HG122_PATCH NW_003871072.2:g.156489G>A
Gene: TTC36, tetratricopeptide repeat domain 36 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TTC36 transcript variant 1 NM_001080441.4:c. N/A Downstream Transcript Variant
TTC36 transcript variant 2 NM_001346096.2:c. N/A Downstream Transcript Variant
TTC36 transcript variant 3 NM_001346097.2:c. N/A Downstream Transcript Variant
TTC36 transcript variant 4 NM_001346098.2:c. N/A Downstream Transcript Variant
Gene: TMEM25, transmembrane protein 25 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TMEM25 transcript variant 2 NM_001144034.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 6 NM_001144035.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 3 NM_001144036.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 4 NM_001144037.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 5 NM_001144038.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 7 NM_001318755.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 8 NM_001318757.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 1 NM_032780.4:c. N/A Upstream Transcript Variant
TMEM25 transcript variant 9 NR_134852.2:n. N/A Upstream Transcript Variant
TMEM25 transcript variant X2 XM_005271703.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X1 XM_006718926.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X13 XM_011543038.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X3 XM_017018422.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X15 XM_017018430.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X32 XM_017018432.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X33 XM_017018433.3:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X14 XM_024448724.2:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X20 XM_047427720.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X21 XM_047427721.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X4 XM_047427722.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X5 XM_047427723.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X6 XM_047427724.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X7 XM_047427725.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X8 XM_047427726.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X9 XM_047427727.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X22 XM_047427728.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X23 XM_047427729.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X24 XM_047427730.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X10 XM_047427731.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X11 XM_047427732.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X12 XM_047427733.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X25 XM_047427734.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X26 XM_047427735.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X27 XM_047427736.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X28 XM_047427737.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X29 XM_047427738.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X30 XM_047427739.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X16 XM_047427740.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X17 XM_047427741.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X18 XM_047427742.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X19 XM_047427743.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X31 XM_047427744.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X34 XM_047427745.1:c. N/A Upstream Transcript Variant
TMEM25 transcript variant X35 XM_047427746.1:c. N/A Upstream Transcript Variant
Gene: TTC36-AS1, TTC36 and KMT2A antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TTC36-AS1 transcript variant 5 NR_120576.1:n.44C>T N/A Non Coding Transcript Variant
TTC36-AS1 transcript variant 1 NR_120572.1:n. N/A Genic Upstream Transcript Variant
TTC36-AS1 transcript variant 2 NR_120573.1:n. N/A Genic Upstream Transcript Variant
TTC36-AS1 transcript variant 3 NR_120574.1:n. N/A Genic Upstream Transcript Variant
TTC36-AS1 transcript variant 4 NR_120575.1:n. N/A Genic 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 11 NC_000011.10:g.118531051= NC_000011.10:g.118531051G>A
GRCh37.p13 chr 11 NC_000011.9:g.118401766= NC_000011.9:g.118401766G>A
GRCh37.p13 chr 11 fix patch HG122_PATCH NW_003871072.2:g.156489= NW_003871072.2:g.156489G>A
TTC36 transcript variant 1 NM_001080441.3:c.*135= NM_001080441.3:c.*135G>A
TTC36 transcript variant 1 NM_001080441.2:c.*135= NM_001080441.2:c.*135G>A
TTC36 transcript variant 2 NM_001346096.1:c.*135= NM_001346096.1:c.*135G>A
TTC36 transcript variant 3 NM_001346097.1:c.*135= NM_001346097.1:c.*135G>A
TTC36 transcript variant 4 NM_001346098.1:c.*135= NM_001346098.1:c.*135G>A
TTC36-AS1 transcript variant 5 NR_120576.1:n.44= NR_120576.1:n.44C>T
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 ss4243471362 Apr 26, 2021 (155)
2 TOPMED ss4901767484 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000011.10 - 118531051 Apr 26, 2021 (155)
4 TopMed NC_000011.10 - 118531051 Apr 26, 2021 (155)
5 ALFA NC_000011.10 - 118531051 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
393452605, 117313140, 13032172665, ss4243471362, ss4901767484 NC_000011.10:118531050:G:A NC_000011.10:118531050: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 rs1391662275

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