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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.

rs1490687889

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:10936147 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CELF2 : Intron Variant
LINC00710 : 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 G=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 C=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 C=0.000004
Allele Frequency Aggregator Total Global 14050 G=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=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 10 NC_000010.11:g.10936147G>C
GRCh37.p13 chr 10 NC_000010.10:g.10978110G>C
Gene: CELF2, CUGBP Elav-like family member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CELF2 transcript variant 5 NM_001326317.2:c.-20+1614…

NM_001326317.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 6 NM_001326318.2:c.-20+1614…

NM_001326318.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 7 NM_001326319.2:c.-57-4270…

NM_001326319.2:c.-57-4270G>C

 		N/A Intron Variant
CELF2 transcript variant 8 NM_001326320.2:c.-20+1614…

NM_001326320.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 9 NM_001326321.2:c.-20+1614…

NM_001326321.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 10 NM_001326323.2:c.-20+1614…

NM_001326323.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 11 NM_001326324.2:c.-20+1614…

NM_001326324.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 12 NM_001326325.2:c.146+1614…

NM_001326325.2:c.146+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 13 NM_001326326.2:c.89+16148…

NM_001326326.2:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 14 NM_001326327.2:c.89+16148…

NM_001326327.2:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 15 NM_001326328.2:c.-20+1614…

NM_001326328.2:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant 1 NM_001025076.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 3 NM_001025077.3:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 4 NM_001083591.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 16 NM_001326329.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 17 NM_001326330.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 18 NM_001326331.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 19 NM_001326332.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 20 NM_001326333.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 21 NM_001326334.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 22 NM_001326335.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 23 NM_001326336.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 24 NM_001326337.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 25 NM_001326338.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 26 NM_001326339.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 27 NM_001326340.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 28 NM_001326341.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 29 NM_001326342.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 30 NM_001326343.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 31 NM_001326344.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 32 NM_001326345.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 33 NM_001326346.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 34 NM_001326347.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 35 NM_001326348.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 36 NM_001326349.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 37 NM_001394502.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 38 NM_001394513.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 39 NM_001394517.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 40 NM_001394518.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 41 NM_001394519.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant 2 NM_006561.4:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X1 XM_047424482.1:c.146+1614…

XM_047424482.1:c.146+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X2 XM_047424483.1:c.146+1614…

XM_047424483.1:c.146+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X4 XM_047424484.1:c.89+16148…

XM_047424484.1:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X5 XM_047424485.1:c.89+16148…

XM_047424485.1:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X7 XM_047424487.1:c.89+16148…

XM_047424487.1:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X8 XM_047424488.1:c.-20+1614…

XM_047424488.1:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X10 XM_047424490.1:c.-20+1614…

XM_047424490.1:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X11 XM_047424491.1:c.-20+1614…

XM_047424491.1:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X12 XM_047424492.1:c.-57-4270…

XM_047424492.1:c.-57-4270G>C

 		N/A Intron Variant
CELF2 transcript variant X14 XM_047424494.1:c.-57-4270…

XM_047424494.1:c.-57-4270G>C

 		N/A Intron Variant
CELF2 transcript variant X16 XM_047424496.1:c.-57-4270…

XM_047424496.1:c.-57-4270G>C

 		N/A Intron Variant
CELF2 transcript variant X18 XM_047424499.1:c.-57-4270…

XM_047424499.1:c.-57-4270G>C

 		N/A Intron Variant
CELF2 transcript variant X29 XM_047424501.1:c.-20+1614…

XM_047424501.1:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X23 XM_047424506.1:c.89+16148…

XM_047424506.1:c.89+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X25 XM_047424508.1:c.-20+1614…

XM_047424508.1:c.-20+16148G>C

 		N/A Intron Variant
CELF2 transcript variant X3 XM_024447776.2:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X6 XM_047424486.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X9 XM_047424489.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X13 XM_047424493.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X15 XM_047424495.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X17 XM_047424498.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X28 XM_047424500.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X19 XM_047424502.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X20 XM_047424503.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X21 XM_047424504.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X22 XM_047424505.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X24 XM_047424507.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X26 XM_047424509.1:c. N/A Genic Upstream Transcript Variant
CELF2 transcript variant X27 XM_047424510.1:c. N/A Genic Upstream Transcript Variant
Gene: LINC00710, long intergenic non-protein coding RNA 710 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC00710 transcript variant 1 NR_015413.1:n. N/A Intron Variant
LINC00710 transcript variant 2 NR_024410.1:n. N/A Intron Variant
LINC00710 transcript variant 3 NR_024411.1: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 G= C
GRCh38.p14 chr 10 NC_000010.11:g.10936147= NC_000010.11:g.10936147G>C
GRCh37.p13 chr 10 NC_000010.10:g.10978110= NC_000010.10:g.10978110G>C
CELF2 transcript variant 5 NM_001326317.2:c.-20+16148= NM_001326317.2:c.-20+16148G>C
CELF2 transcript variant 6 NM_001326318.2:c.-20+16148= NM_001326318.2:c.-20+16148G>C
CELF2 transcript variant 7 NM_001326319.2:c.-57-4270= NM_001326319.2:c.-57-4270G>C
CELF2 transcript variant 8 NM_001326320.2:c.-20+16148= NM_001326320.2:c.-20+16148G>C
CELF2 transcript variant 9 NM_001326321.2:c.-20+16148= NM_001326321.2:c.-20+16148G>C
CELF2 transcript variant 10 NM_001326323.2:c.-20+16148= NM_001326323.2:c.-20+16148G>C
CELF2 transcript variant 11 NM_001326324.2:c.-20+16148= NM_001326324.2:c.-20+16148G>C
CELF2 transcript variant 12 NM_001326325.2:c.146+16148= NM_001326325.2:c.146+16148G>C
CELF2 transcript variant 13 NM_001326326.2:c.89+16148= NM_001326326.2:c.89+16148G>C
CELF2 transcript variant 14 NM_001326327.2:c.89+16148= NM_001326327.2:c.89+16148G>C
CELF2 transcript variant 15 NM_001326328.2:c.-20+16148= NM_001326328.2:c.-20+16148G>C
CELF2 transcript variant X1 XM_005252346.1:c.146+16148= XM_005252346.1:c.146+16148G>C
CELF2 transcript variant X2 XM_005252347.1:c.146+16148= XM_005252347.1:c.146+16148G>C
CELF2 transcript variant X3 XM_005252348.1:c.146+16148= XM_005252348.1:c.146+16148G>C
CELF2 transcript variant X4 XM_005252349.1:c.146+16148= XM_005252349.1:c.146+16148G>C
CELF2 transcript variant X5 XM_005252350.1:c.146+16148= XM_005252350.1:c.146+16148G>C
CELF2 transcript variant X6 XM_005252351.1:c.146+16148= XM_005252351.1:c.146+16148G>C
CELF2 transcript variant X1 XM_047424482.1:c.146+16148= XM_047424482.1:c.146+16148G>C
CELF2 transcript variant X2 XM_047424483.1:c.146+16148= XM_047424483.1:c.146+16148G>C
CELF2 transcript variant X4 XM_047424484.1:c.89+16148= XM_047424484.1:c.89+16148G>C
CELF2 transcript variant X5 XM_047424485.1:c.89+16148= XM_047424485.1:c.89+16148G>C
CELF2 transcript variant X7 XM_047424487.1:c.89+16148= XM_047424487.1:c.89+16148G>C
CELF2 transcript variant X8 XM_047424488.1:c.-20+16148= XM_047424488.1:c.-20+16148G>C
CELF2 transcript variant X10 XM_047424490.1:c.-20+16148= XM_047424490.1:c.-20+16148G>C
CELF2 transcript variant X11 XM_047424491.1:c.-20+16148= XM_047424491.1:c.-20+16148G>C
CELF2 transcript variant X12 XM_047424492.1:c.-57-4270= XM_047424492.1:c.-57-4270G>C
CELF2 transcript variant X14 XM_047424494.1:c.-57-4270= XM_047424494.1:c.-57-4270G>C
CELF2 transcript variant X16 XM_047424496.1:c.-57-4270= XM_047424496.1:c.-57-4270G>C
CELF2 transcript variant X18 XM_047424499.1:c.-57-4270= XM_047424499.1:c.-57-4270G>C
CELF2 transcript variant X29 XM_047424501.1:c.-20+16148= XM_047424501.1:c.-20+16148G>C
CELF2 transcript variant X23 XM_047424506.1:c.89+16148= XM_047424506.1:c.89+16148G>C
CELF2 transcript variant X25 XM_047424508.1:c.-20+16148= XM_047424508.1:c.-20+16148G>C
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss4842444157 Apr 27, 2021 (155)
2 TopMed NC_000010.11 - 10936147 Apr 27, 2021 (155)
3 ALFA NC_000010.11 - 10936147 Apr 27, 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
57989812, 7749381710, ss4842444157 NC_000010.11:10936146:G:C NC_000010.11:10936146:G:C (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 rs1490687889

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