Name: rs1490074472
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.

rs1490074472

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:10947174 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000007 (1/140302, GnomAD)
T=0.00000 (0/10680, 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	HWEP
Total	Global	10680	A=1.00000	T=0.00000	1.0	N/A
European	Sub	6962	A=1.0000	T=0.0000	1.0	N/A
African	Sub	2294	A=1.0000	T=0.0000	1.0	N/A
African Others	Sub	84	A=1.00	T=0.00	1.0	N/A
African American	Sub	2210	A=1.0000	T=0.0000	1.0	N/A
Asian	Sub	108	A=1.000	T=0.000	1.0	N/A
East Asian	Sub	84	A=1.00	T=0.00	1.0	N/A
Other Asian	Sub	24	A=1.00	T=0.00	1.0	N/A
Latin American 1	Sub	146	A=1.000	T=0.000	1.0	N/A
Latin American 2	Sub	610	A=1.000	T=0.000	1.0	N/A
South Asian	Sub	94	A=1.00	T=0.00	1.0	N/A
Other	Sub	466	A=1.000	T=0.000	1.0	N/A

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
gnomAD - Genomes	Global	Study-wide	140302	A=0.999993	T=0.000007
gnomAD - Genomes	European	Sub	75972	A=1.00000	T=0.00000
gnomAD - Genomes	African	Sub	42060	A=0.99998	T=0.00002
gnomAD - Genomes	American	Sub	13662	A=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3130	A=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2154	A=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	10680	A=1.00000	T=0.00000
Allele Frequency Aggregator	European	Sub	6962	A=1.0000	T=0.0000
Allele Frequency Aggregator	African	Sub	2294	A=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=1.000	T=0.000
Allele Frequency Aggregator	Other	Sub	466	A=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	108	A=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	A=1.00	T=0.00

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.10947174A>T
GRCh37.p13 chr 10	NC_000010.10:g.10989137A>T

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+2717… NM_001326317.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 6	NM_001326318.2:c.-20+2717… NM_001326318.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 7	NM_001326319.2:c.-20+6720… NM_001326319.2:c.-20+6720A>T	N/A	Intron Variant
CELF2 transcript variant 8	NM_001326320.2:c.-20+2717… NM_001326320.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 9	NM_001326321.2:c.-20+2717… NM_001326321.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 10	NM_001326323.2:c.-20+2717… NM_001326323.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 11	NM_001326324.2:c.-20+2717… NM_001326324.2:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant 12	NM_001326325.2:c.146+2717… NM_001326325.2:c.146+27175A>T	N/A	Intron Variant
CELF2 transcript variant 13	NM_001326326.2:c.89+27175… NM_001326326.2:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant 14	NM_001326327.2:c.89+27175… NM_001326327.2:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant 15	NM_001326328.2:c.-20+2717… NM_001326328.2:c.-20+27175A>T	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+2717… XM_047424482.1:c.146+27175A>T	N/A	Intron Variant
CELF2 transcript variant X2	XM_047424483.1:c.146+2717… XM_047424483.1:c.146+27175A>T	N/A	Intron Variant
CELF2 transcript variant X4	XM_047424484.1:c.89+27175… XM_047424484.1:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant X5	XM_047424485.1:c.89+27175… XM_047424485.1:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant X7	XM_047424487.1:c.89+27175… XM_047424487.1:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant X8	XM_047424488.1:c.-20+2717… XM_047424488.1:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant X10	XM_047424490.1:c.-20+2717… XM_047424490.1:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant X11	XM_047424491.1:c.-20+2717… XM_047424491.1:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant X12	XM_047424492.1:c.-20+6720… XM_047424492.1:c.-20+6720A>T	N/A	Intron Variant
CELF2 transcript variant X14	XM_047424494.1:c.-20+6720… XM_047424494.1:c.-20+6720A>T	N/A	Intron Variant
CELF2 transcript variant X16	XM_047424496.1:c.-20+6720… XM_047424496.1:c.-20+6720A>T	N/A	Intron Variant
CELF2 transcript variant X18	XM_047424499.1:c.-20+6720… XM_047424499.1:c.-20+6720A>T	N/A	Intron Variant
CELF2 transcript variant X29	XM_047424501.1:c.-20+2717… XM_047424501.1:c.-20+27175A>T	N/A	Intron Variant
CELF2 transcript variant X23	XM_047424506.1:c.89+27175… XM_047424506.1:c.89+27175A>T	N/A	Intron Variant
CELF2 transcript variant X25	XM_047424508.1:c.-20+2717… XM_047424508.1:c.-20+27175A>T	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

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=	T
GRCh38.p14 chr 10	NC_000010.11:g.10947174=	NC_000010.11:g.10947174A>T
GRCh37.p13 chr 10	NC_000010.10:g.10989137=	NC_000010.10:g.10989137A>T
CELF2 transcript variant 5	NM_001326317.2:c.-20+27175=	NM_001326317.2:c.-20+27175A>T
CELF2 transcript variant 6	NM_001326318.2:c.-20+27175=	NM_001326318.2:c.-20+27175A>T
CELF2 transcript variant 7	NM_001326319.2:c.-20+6720=	NM_001326319.2:c.-20+6720A>T
CELF2 transcript variant 8	NM_001326320.2:c.-20+27175=	NM_001326320.2:c.-20+27175A>T
CELF2 transcript variant 9	NM_001326321.2:c.-20+27175=	NM_001326321.2:c.-20+27175A>T
CELF2 transcript variant 10	NM_001326323.2:c.-20+27175=	NM_001326323.2:c.-20+27175A>T
CELF2 transcript variant 11	NM_001326324.2:c.-20+27175=	NM_001326324.2:c.-20+27175A>T
CELF2 transcript variant 12	NM_001326325.2:c.146+27175=	NM_001326325.2:c.146+27175A>T
CELF2 transcript variant 13	NM_001326326.2:c.89+27175=	NM_001326326.2:c.89+27175A>T
CELF2 transcript variant 14	NM_001326327.2:c.89+27175=	NM_001326327.2:c.89+27175A>T
CELF2 transcript variant 15	NM_001326328.2:c.-20+27175=	NM_001326328.2:c.-20+27175A>T
CELF2 transcript variant X1	XM_005252346.1:c.146+27175=	XM_005252346.1:c.146+27175A>T
CELF2 transcript variant X2	XM_005252347.1:c.146+27175=	XM_005252347.1:c.146+27175A>T
CELF2 transcript variant X3	XM_005252348.1:c.146+27175=	XM_005252348.1:c.146+27175A>T
CELF2 transcript variant X4	XM_005252349.1:c.146+27175=	XM_005252349.1:c.146+27175A>T
CELF2 transcript variant X5	XM_005252350.1:c.146+27175=	XM_005252350.1:c.146+27175A>T
CELF2 transcript variant X6	XM_005252351.1:c.146+27175=	XM_005252351.1:c.146+27175A>T
CELF2 transcript variant X1	XM_047424482.1:c.146+27175=	XM_047424482.1:c.146+27175A>T
CELF2 transcript variant X2	XM_047424483.1:c.146+27175=	XM_047424483.1:c.146+27175A>T
CELF2 transcript variant X4	XM_047424484.1:c.89+27175=	XM_047424484.1:c.89+27175A>T
CELF2 transcript variant X5	XM_047424485.1:c.89+27175=	XM_047424485.1:c.89+27175A>T
CELF2 transcript variant X7	XM_047424487.1:c.89+27175=	XM_047424487.1:c.89+27175A>T
CELF2 transcript variant X8	XM_047424488.1:c.-20+27175=	XM_047424488.1:c.-20+27175A>T
CELF2 transcript variant X10	XM_047424490.1:c.-20+27175=	XM_047424490.1:c.-20+27175A>T
CELF2 transcript variant X11	XM_047424491.1:c.-20+27175=	XM_047424491.1:c.-20+27175A>T
CELF2 transcript variant X12	XM_047424492.1:c.-20+6720=	XM_047424492.1:c.-20+6720A>T
CELF2 transcript variant X14	XM_047424494.1:c.-20+6720=	XM_047424494.1:c.-20+6720A>T
CELF2 transcript variant X16	XM_047424496.1:c.-20+6720=	XM_047424496.1:c.-20+6720A>T
CELF2 transcript variant X18	XM_047424499.1:c.-20+6720=	XM_047424499.1:c.-20+6720A>T
CELF2 transcript variant X29	XM_047424501.1:c.-20+27175=	XM_047424501.1:c.-20+27175A>T
CELF2 transcript variant X23	XM_047424506.1:c.89+27175=	XM_047424506.1:c.89+27175A>T
CELF2 transcript variant X25	XM_047424508.1:c.-20+27175=	XM_047424508.1:c.-20+27175A>T

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	GNOMAD	ss2885506276	Nov 08, 2017 (151)
2	gnomAD - Genomes	NC_000010.11 - 10947174	Apr 27, 2021 (155)
3	ALFA	NC_000010.11 - 10947174	Apr 27, 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
ss2885506276	NC_000010.10:10989136:A:T	NC_000010.11:10947173:A:T	(self)
343443257, 2878682951	NC_000010.11:10947173:A:T	NC_000010.11:10947173:A:T	(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 rs1490074472

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1490074472