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dbSNP Short Genetic Variations

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.

rs1491458392

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:143395270-143395273 (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
delCT
Variation Type
Indel Insertion and Deletion
Frequency
delCT=0.000049 (13/264690, TOPMED)
delCT=0.000072 (18/251076, GnomAD_exome)
delCT=0.000043 (6/140272, GnomAD) (+ 3 more)
delCT=0.000049 (6/121406, ExAC)
delCT=0.00021 (3/14050, ALFA)
delCT=0.00008 (1/12516, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPHA1 : 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 CTCT=0.99979 CT=0.00021 0.999573 0.0 0.000427 0
European Sub 9690 CTCT=0.9999 CT=0.0001 0.999794 0.0 0.000206 0
African Sub 2898 CTCT=1.0000 CT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CTCT=1.000 CT=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CTCT=1.0000 CT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CTCT=1.000 CT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CTCT=1.00 CT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CTCT=1.00 CT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CTCT=0.986 CT=0.014 0.972603 0.0 0.027397 0
Latin American 2 Sub 610 CTCT=1.000 CT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CTCT=1.00 CT=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CTCT=1.000 CT=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 CTCT=0.999951 delCT=0.000049
gnomAD - Exomes Global Study-wide 251076 CTCT=0.999928 delCT=0.000072
gnomAD - Exomes European Sub 135018 CTCT=0.999904 delCT=0.000096
gnomAD - Exomes Asian Sub 49008 CTCT=0.99996 delCT=0.00004
gnomAD - Exomes American Sub 34586 CTCT=0.99991 delCT=0.00009
gnomAD - Exomes African Sub 16256 CTCT=1.00000 delCT=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 CTCT=1.00000 delCT=0.00000
gnomAD - Exomes Other Sub 6134 CTCT=1.0000 delCT=0.0000
gnomAD - Genomes Global Study-wide 140272 CTCT=0.999957 delCT=0.000043
gnomAD - Genomes European Sub 75950 CTCT=0.99992 delCT=0.00008
gnomAD - Genomes African Sub 42050 CTCT=1.00000 delCT=0.00000
gnomAD - Genomes American Sub 13664 CTCT=1.00000 delCT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 CTCT=1.0000 delCT=0.0000
gnomAD - Genomes East Asian Sub 3134 CTCT=1.0000 delCT=0.0000
gnomAD - Genomes Other Sub 2154 CTCT=1.0000 delCT=0.0000
ExAC Global Study-wide 121406 CTCT=0.999951 delCT=0.000049
ExAC Europe Sub 73352 CTCT=0.99995 delCT=0.00005
ExAC Asian Sub 25164 CTCT=0.99996 delCT=0.00004
ExAC American Sub 11578 CTCT=0.99991 delCT=0.00009
ExAC African Sub 10404 CTCT=1.00000 delCT=0.00000
ExAC Other Sub 908 CTCT=1.000 delCT=0.000
Allele Frequency Aggregator Total Global 14050 CTCT=0.99979 delCT=0.00021
Allele Frequency Aggregator European Sub 9690 CTCT=0.9999 delCT=0.0001
Allele Frequency Aggregator African Sub 2898 CTCT=1.0000 delCT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CTCT=1.000 delCT=0.000
Allele Frequency Aggregator Other Sub 496 CTCT=1.000 delCT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CTCT=0.986 delCT=0.014
Allele Frequency Aggregator Asian Sub 112 CTCT=1.000 delCT=0.000
Allele Frequency Aggregator South Asian Sub 98 CTCT=1.00 delCT=0.00
GO Exome Sequencing Project Global Study-wide 12516 CTCT=0.99992 delCT=0.00008
GO Exome Sequencing Project European American Sub 8252 CTCT=0.9999 delCT=0.0001
GO Exome Sequencing Project African American Sub 4264 CTCT=1.0000 delCT=0.0000
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 7 NC_000007.14:g.143395270CT[1]
GRCh37.p13 chr 7 NC_000007.13:g.143092363CT[1]
GRCh38.p14 chr 7 fix patch HG708_PATCH NW_018654714.1:g.14634CT[1]
Gene: EPHA1, EPH receptor A1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPHA1 transcript NM_005232.5:c.2083+48_208…

NM_005232.5:c.2083+48_2083+49del

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 CTCT= delCT
GRCh38.p14 chr 7 NC_000007.14:g.143395270_143395273= NC_000007.14:g.143395270CT[1]
GRCh37.p13 chr 7 NC_000007.13:g.143092363_143092366= NC_000007.13:g.143092363CT[1]
GRCh38.p14 chr 7 fix patch HG708_PATCH NW_018654714.1:g.14634_14637= NW_018654714.1:g.14634CT[1]
EPHA1 transcript NM_005232.4:c.2083+49= NM_005232.4:c.2083+48_2083+49del
EPHA1 transcript NM_005232.5:c.2083+49= NM_005232.5:c.2083+48_2083+49del
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#.

6 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711874796 Jan 10, 2018 (151)
2 GNOMAD ss2736849657 Jan 10, 2018 (151)
3 GNOMAD ss2747950163 Jan 10, 2018 (151)
4 GNOMAD ss2860229653 Jan 10, 2018 (151)
5 EVA ss3824328682 Apr 26, 2020 (154)
6 TOPMED ss4767179180 Apr 26, 2021 (155)
7 ExAC NC_000007.13 - 143092363 Oct 12, 2018 (152)
8 gnomAD - Genomes NC_000007.14 - 143395270 Apr 26, 2021 (155)
9 gnomAD - Exomes NC_000007.13 - 143092363 Jul 13, 2019 (153)
10 GO Exome Sequencing Project NC_000007.13 - 143092363 Oct 12, 2018 (152)
11 TopMed NC_000007.14 - 143395270 Apr 26, 2021 (155)
12 ALFA NC_000007.14 - 143395270 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
9086525, 6015673, 786551, ss1711874796, ss2736849657, ss2747950163, ss2860229653, ss3824328682 NC_000007.13:143092362:CT: NC_000007.14:143395269:CTCT:CT (self)
279540109, 604556739, ss4767179180 NC_000007.14:143395269:CT: NC_000007.14:143395269:CTCT:CT (self)
1754593005 NC_000007.14:143395269:CTCT:CT NC_000007.14:143395269:CTCT:CT (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 rs1491458392

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