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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.

rs763298549

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:14735471-14735475 (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
delCTTT
Variation Type
Indel Insertion and Deletion
Frequency
delCTTT=0.000049 (13/264690, TOPMED)
delCTTT=0.000036 (5/140252, GnomAD)
delCTTT=0.00011 (3/28258, 14KJPN) (+ 4 more)
delCTTT=0.00012 (2/16760, 8.3KJPN)
delCTTT=0.00007 (1/14050, ALFA)
delCTTT=0.0000 (0/3854, ALSPAC)
delCTTT=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 TCTTT=0.99993 T=0.00007
European Sub 9690 TCTTT=0.9999 T=0.0001
African Sub 2898 TCTTT=1.0000 T=0.0000
African Others Sub 114 TCTTT=1.000 T=0.000
African American Sub 2784 TCTTT=1.0000 T=0.0000
Asian Sub 112 TCTTT=1.000 T=0.000
East Asian Sub 86 TCTTT=1.00 T=0.00
Other Asian Sub 26 TCTTT=1.00 T=0.00
Latin American 1 Sub 146 TCTTT=1.000 T=0.000
Latin American 2 Sub 610 TCTTT=1.000 T=0.000
South Asian Sub 98 TCTTT=1.00 T=0.00
Other Sub 496 TCTTT=1.000 T=0.000


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 TCTTT=0.999951 delCTTT=0.000049
gnomAD - Genomes Global Study-wide 140252 TCTTT=0.999964 delCTTT=0.000036
gnomAD - Genomes European Sub 75948 TCTTT=0.99997 delCTTT=0.00003
gnomAD - Genomes African Sub 42050 TCTTT=0.99998 delCTTT=0.00002
gnomAD - Genomes American Sub 13650 TCTTT=1.00000 delCTTT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 TCTTT=1.0000 delCTTT=0.0000
gnomAD - Genomes East Asian Sub 3134 TCTTT=0.9994 delCTTT=0.0006
gnomAD - Genomes Other Sub 2148 TCTTT=1.0000 delCTTT=0.0000
14KJPN JAPANESE Study-wide 28258 TCTTT=0.99989 delCTTT=0.00011
8.3KJPN JAPANESE Study-wide 16760 TCTTT=0.99988 delCTTT=0.00012
Allele Frequency Aggregator Total Global 14050 TCTTT=0.99993 delCTTT=0.00007
Allele Frequency Aggregator European Sub 9690 TCTTT=0.9999 delCTTT=0.0001
Allele Frequency Aggregator African Sub 2898 TCTTT=1.0000 delCTTT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TCTTT=1.000 delCTTT=0.000
Allele Frequency Aggregator Other Sub 496 TCTTT=1.000 delCTTT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TCTTT=1.000 delCTTT=0.000
Allele Frequency Aggregator Asian Sub 112 TCTTT=1.000 delCTTT=0.000
Allele Frequency Aggregator South Asian Sub 98 TCTTT=1.00 delCTTT=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 TCTTT=1.0000 delCTTT=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 TCTTT=0.9997 delCTTT=0.0003
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 9 NC_000009.12:g.14735472_14735475del
GRCh37.p13 chr 9 NC_000009.11:g.14735470_14735473del
FREM1 RefSeqGene NG_017005.2:g.179763_179766del
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 TCTTT= delCTTT
GRCh38.p14 chr 9 NC_000009.12:g.14735471_14735475= NC_000009.12:g.14735472_14735475del
GRCh37.p13 chr 9 NC_000009.11:g.14735469_14735473= NC_000009.11:g.14735470_14735473del
FREM1 RefSeqGene NG_017005.2:g.179762_179766= NG_017005.2:g.179763_179766del
FREM1 transcript variant 1 NM_144966.5:c.*1921_*1925= NM_144966.5:c.*1922_*1925del
FREM1 transcript variant 1 NM_144966.6:c.*1921_*1925= NM_144966.6:c.*1922_*1925del
FREM1 transcript variant 2 NM_001177704.2:c.*1921_*1925= NM_001177704.2:c.*1922_*1925del
FREM1 transcript variant 9 NR_163239.1:n.9269_9273= NR_163239.1:n.9270_9273del
FREM1 transcript variant 13 NM_001379081.1:c.*1921_*1925= NM_001379081.1:c.*1922_*1925del
FREM1 transcript variant 8 NR_163238.1:n.7851_7855= NR_163238.1:n.7852_7855del
FREM1 transcript variant 3 NM_001370058.1:c.*2072_*2076= NM_001370058.1:c.*2073_*2076del
FREM1 transcript variant 5 NM_001370061.1:c.*1921_*1925= NM_001370061.1:c.*1922_*1925del
FREM1 transcript variant 12 NR_163242.1:n.4283_4287= NR_163242.1:n.4284_4287del
FREM1 transcript variant 2 NM_001177704.1:c.*1921_*1925= NM_001177704.1:c.*1922_*1925del
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, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1706336348 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1706336381 Apr 01, 2015 (144)
3 GNOMAD ss2875811802 Nov 08, 2017 (151)
4 TOPMED ss4813801437 Apr 26, 2021 (155)
5 TOMMO_GENOMICS ss5192234540 Apr 26, 2021 (155)
6 TOMMO_GENOMICS ss5735325080 Oct 16, 2022 (156)
7 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 14735469 Oct 12, 2018 (152)
8 gnomAD - Genomes NC_000009.12 - 14735471 Apr 26, 2021 (155)
9 8.3KJPN NC_000009.11 - 14735469 Apr 26, 2021 (155)
10 14KJPN NC_000009.12 - 14735471 Oct 16, 2022 (156)
11 TopMed NC_000009.12 - 14735471 Apr 26, 2021 (155)
12 UK 10K study - Twins NC_000009.11 - 14735469 Oct 12, 2018 (152)
13 ALFA NC_000009.12 - 14735471 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
25187778, 50203847, 25187778, ss1706336348, ss1706336381, ss2875811802, ss5192234540 NC_000009.11:14735468:TCTT: NC_000009.12:14735470:TCTTT:T (self)
319101802, 69162184, 651178998, ss4813801437, ss5735325080 NC_000009.12:14735470:TCTT: NC_000009.12:14735470:TCTTT:T (self)
10419172635 NC_000009.12:14735470:TCTTT:T NC_000009.12:14735470:TCTTT:T (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 rs763298549

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.post761+d5e8e07