Name: rs1257335460
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.

rs1257335460

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:139151081-139151083 (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: delAA / delA / dupA / dupAA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.000017 (2/116920, GnomAD)
delAA=0.00000 (0/11860, ALFA)
delA=0.00000 (0/11860, ALFA) (+ 2 more)
dupA=0.00000 (0/11860, ALFA)
dupAA=0.00000 (0/11860, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ELF2 : 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	11860	AAA=1.00000	A=0.00000, AA=0.00000, AAAA=0.00000, AAAAA=0.00000	1.0	N/A
European	Sub	7616	AAA=1.0000	A=0.0000, AA=0.0000, AAAA=0.0000, AAAAA=0.0000	1.0	N/A
African	Sub	2816	AAA=1.0000	A=0.0000, AA=0.0000, AAAA=0.0000, AAAAA=0.0000	1.0	N/A
African Others	Sub	108	AAA=1.000	A=0.000, AA=0.000, AAAA=0.000, AAAAA=0.000	1.0	N/A
African American	Sub	2708	AAA=1.0000	A=0.0000, AA=0.0000, AAAA=0.0000, AAAAA=0.0000	1.0	N/A
Asian	Sub	108	AAA=1.000	A=0.000, AA=0.000, AAAA=0.000, AAAAA=0.000	1.0	N/A
East Asian	Sub	84	AAA=1.00	A=0.00, AA=0.00, AAAA=0.00, AAAAA=0.00	1.0	N/A
Other Asian	Sub	24	AAA=1.00	A=0.00, AA=0.00, AAAA=0.00, AAAAA=0.00	1.0	N/A
Latin American 1	Sub	146	AAA=1.000	A=0.000, AA=0.000, AAAA=0.000, AAAAA=0.000	1.0	N/A
Latin American 2	Sub	610	AAA=1.000	A=0.000, AA=0.000, AAAA=0.000, AAAAA=0.000	1.0	N/A
South Asian	Sub	94	AAA=1.00	A=0.00, AA=0.00, AAAA=0.00, AAAAA=0.00	1.0	N/A
Other	Sub	470	AAA=1.000	A=0.000, AA=0.000, AAAA=0.000, AAAAA=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	116920	AAA=0.999983	delA=0.000017
gnomAD - Genomes	European	Sub	64024	AAA=1.00000	delA=0.00000
gnomAD - Genomes	African	Sub	34918	AAA=0.99994	delA=0.00006
gnomAD - Genomes	American	Sub	11038	AAA=1.00000	delA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	2674	AAA=1.0000	delA=0.0000
gnomAD - Genomes	East Asian	Sub	2480	AAA=1.0000	delA=0.0000
gnomAD - Genomes	Other	Sub	1786	AAA=1.0000	delA=0.0000
Allele Frequency Aggregator	Total	Global	11860	AAA=1.00000	delAA=0.00000, delA=0.00000, dupA=0.00000, dupAA=0.00000
Allele Frequency Aggregator	European	Sub	7616	AAA=1.0000	delAA=0.0000, delA=0.0000, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator	African	Sub	2816	AAA=1.0000	delAA=0.0000, delA=0.0000, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	AAA=1.000	delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Other	Sub	470	AAA=1.000	delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	AAA=1.000	delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Asian	Sub	108	AAA=1.000	delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	AAA=1.00	delAA=0.00, delA=0.00, dupA=0.00, dupAA=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 4	NC_000004.12:g.139151082_139151083del
GRCh38.p14 chr 4	NC_000004.12:g.139151083del
GRCh38.p14 chr 4	NC_000004.12:g.139151083dup
GRCh38.p14 chr 4	NC_000004.12:g.139151082_139151083dup
GRCh37.p13 chr 4	NC_000004.11:g.140072236_140072237del
GRCh37.p13 chr 4	NC_000004.11:g.140072237del
GRCh37.p13 chr 4	NC_000004.11:g.140072237dup
GRCh37.p13 chr 4	NC_000004.11:g.140072236_140072237dup

Gene: ELF2, E74 like ETS transcription factor 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ELF2 transcript variant 6	NM_001331036.3:c.-251-115… NM_001331036.3:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant 7	NM_001371324.1:c.-251-115… NM_001371324.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant 8	NM_001371336.1:c.-251-115… NM_001371336.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant 9	NM_001371337.1:c.-722-115… NM_001371337.1:c.-722-11585_-722-11584del	N/A	Intron Variant
ELF2 transcript variant 10	NM_001371338.1:c.-722-115… NM_001371338.1:c.-722-11585_-722-11584del	N/A	Intron Variant
ELF2 transcript variant 11	NM_001371339.1:c.-666-115… NM_001371339.1:c.-666-11585_-666-11584del	N/A	Intron Variant
ELF2 transcript variant 1	NM_201999.3:c.-251-11585_… NM_201999.3:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant 3	NM_001276457.2:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant 4	NM_001276458.3:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant 5	NM_001276459.3:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant 2	NM_006874.5:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant X10	XM_005262805.3:c.-251-115… XM_005262805.3:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X2	XM_047449733.1:c.-251-115… XM_047449733.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X3	XM_047449734.1:c.-251-115… XM_047449734.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X4	XM_047449736.1:c.-251-115… XM_047449736.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X5	XM_047449737.1:c.-251-115… XM_047449737.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X6	XM_047449738.1:c.-251-115… XM_047449738.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X8	XM_047449740.1:c.-251-115… XM_047449740.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X9	XM_047449741.1:c.-251-115… XM_047449741.1:c.-251-11585_-251-11584del	N/A	Intron Variant
ELF2 transcript variant X11	XM_011531711.3:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant X13	XM_011531714.3:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant X1	XM_047449732.1:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant X7	XM_047449739.1:c.	N/A	Genic Upstream Transcript Variant
ELF2 transcript variant X12	XM_047449742.1:c.	N/A	Genic Upstream Transcript 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	AAA=	delAA	delA	dupA	dupAA
GRCh38.p14 chr 4	NC_000004.12:g.139151081_139151083=	NC_000004.12:g.139151082_139151083del	NC_000004.12:g.139151083del	NC_000004.12:g.139151083dup	NC_000004.12:g.139151082_139151083dup
GRCh37.p13 chr 4	NC_000004.11:g.140072235_140072237=	NC_000004.11:g.140072236_140072237del	NC_000004.11:g.140072237del	NC_000004.11:g.140072237dup	NC_000004.11:g.140072236_140072237dup
ELF2 transcript variant 6	NM_001331036.3:c.-251-11584=	NM_001331036.3:c.-251-11585_-251-11584del	NM_001331036.3:c.-251-11584del	NM_001331036.3:c.-251-11584dup	NM_001331036.3:c.-251-11585_-251-11584dup
ELF2 transcript variant 7	NM_001371324.1:c.-251-11584=	NM_001371324.1:c.-251-11585_-251-11584del	NM_001371324.1:c.-251-11584del	NM_001371324.1:c.-251-11584dup	NM_001371324.1:c.-251-11585_-251-11584dup
ELF2 transcript variant 8	NM_001371336.1:c.-251-11584=	NM_001371336.1:c.-251-11585_-251-11584del	NM_001371336.1:c.-251-11584del	NM_001371336.1:c.-251-11584dup	NM_001371336.1:c.-251-11585_-251-11584dup
ELF2 transcript variant 9	NM_001371337.1:c.-722-11584=	NM_001371337.1:c.-722-11585_-722-11584del	NM_001371337.1:c.-722-11584del	NM_001371337.1:c.-722-11584dup	NM_001371337.1:c.-722-11585_-722-11584dup
ELF2 transcript variant 10	NM_001371338.1:c.-722-11584=	NM_001371338.1:c.-722-11585_-722-11584del	NM_001371338.1:c.-722-11584del	NM_001371338.1:c.-722-11584dup	NM_001371338.1:c.-722-11585_-722-11584dup
ELF2 transcript variant 11	NM_001371339.1:c.-666-11584=	NM_001371339.1:c.-666-11585_-666-11584del	NM_001371339.1:c.-666-11584del	NM_001371339.1:c.-666-11584dup	NM_001371339.1:c.-666-11585_-666-11584dup
ELF2 transcript variant 1	NM_201999.3:c.-251-11584=	NM_201999.3:c.-251-11585_-251-11584del	NM_201999.3:c.-251-11584del	NM_201999.3:c.-251-11584dup	NM_201999.3:c.-251-11585_-251-11584dup
ELF2 transcript variant X1	XM_005262803.1:c.-251-11584=	XM_005262803.1:c.-251-11585_-251-11584del	XM_005262803.1:c.-251-11584del	XM_005262803.1:c.-251-11584dup	XM_005262803.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X2	XM_005262804.1:c.-251-11584=	XM_005262804.1:c.-251-11585_-251-11584del	XM_005262804.1:c.-251-11584del	XM_005262804.1:c.-251-11584dup	XM_005262804.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X4	XM_005262805.1:c.-251-11584=	XM_005262805.1:c.-251-11585_-251-11584del	XM_005262805.1:c.-251-11584del	XM_005262805.1:c.-251-11584dup	XM_005262805.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X10	XM_005262805.3:c.-251-11584=	XM_005262805.3:c.-251-11585_-251-11584del	XM_005262805.3:c.-251-11584del	XM_005262805.3:c.-251-11584dup	XM_005262805.3:c.-251-11585_-251-11584dup
ELF2 transcript variant X2	XM_047449733.1:c.-251-11584=	XM_047449733.1:c.-251-11585_-251-11584del	XM_047449733.1:c.-251-11584del	XM_047449733.1:c.-251-11584dup	XM_047449733.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X3	XM_047449734.1:c.-251-11584=	XM_047449734.1:c.-251-11585_-251-11584del	XM_047449734.1:c.-251-11584del	XM_047449734.1:c.-251-11584dup	XM_047449734.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X4	XM_047449736.1:c.-251-11584=	XM_047449736.1:c.-251-11585_-251-11584del	XM_047449736.1:c.-251-11584del	XM_047449736.1:c.-251-11584dup	XM_047449736.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X5	XM_047449737.1:c.-251-11584=	XM_047449737.1:c.-251-11585_-251-11584del	XM_047449737.1:c.-251-11584del	XM_047449737.1:c.-251-11584dup	XM_047449737.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X6	XM_047449738.1:c.-251-11584=	XM_047449738.1:c.-251-11585_-251-11584del	XM_047449738.1:c.-251-11584del	XM_047449738.1:c.-251-11584dup	XM_047449738.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X8	XM_047449740.1:c.-251-11584=	XM_047449740.1:c.-251-11585_-251-11584del	XM_047449740.1:c.-251-11584del	XM_047449740.1:c.-251-11584dup	XM_047449740.1:c.-251-11585_-251-11584dup
ELF2 transcript variant X9	XM_047449741.1:c.-251-11584=	XM_047449741.1:c.-251-11585_-251-11584del	XM_047449741.1:c.-251-11584del	XM_047449741.1:c.-251-11584dup	XM_047449741.1:c.-251-11585_-251-11584dup

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	ss4121583378	Apr 26, 2021 (155)
2	gnomAD - Genomes	NC_000004.12 - 139151081	Apr 26, 2021 (155)
3	ALFA	NC_000004.12 - 139151081	Apr 26, 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
948988641	NC_000004.12:139151080:AAA:A	NC_000004.12:139151080:AAA:A	(self)
166927444, ss4121583378	NC_000004.12:139151080:A:	NC_000004.12:139151080:AAA:AA	(self)
948988641	NC_000004.12:139151080:AAA:AA	NC_000004.12:139151080:AAA:AA	(self)
948988641	NC_000004.12:139151080:AAA:AAAA	NC_000004.12:139151080:AAA:AAAA	(self)
948988641	NC_000004.12:139151080:AAA:AAAAA	NC_000004.12:139151080:AAA:AAAAA	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss3444516176	NC_000004.12:139151080::A	NC_000004.12:139151080:AAA:AAAA
ss3444516178	NC_000004.12:139151080:AA:	NC_000004.12:139151080:AAA:A

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

No publications for rs1257335460

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1257335460