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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.

rs142228782

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr5:132873473-132873479 (GRCh38.p13) 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
delCTCA / dupCTCA
Variation Type
Indel Insertion and Deletion
Frequency
delCTCA=0.107968 (28578/264690, TOPMED)
delCTCA=0.111516 (15627/140132, GnomAD)
delCTCA=0.13467 (2494/18520, ALFA) (+ 9 more)
delCTCA=0.12476 (2091/16760, 8.3KJPN)
delCTCA=0.1054 (528/5008, 1000G)
delCTCA=0.1511 (677/4480, Estonian)
delCTCA=0.1593 (614/3854, ALSPAC)
delCTCA=0.1567 (581/3708, TWINSUK)
delCTCA=0.1365 (250/1832, Korea1K)
delCTCA=0.195 (195/998, GoNL)
delCTCA=0.170 (102/600, NorthernSweden)
delCTCA=0.23 (9/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LEAP2 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 5 NC_000005.10:g.132873476_132873479del
GRCh38.p13 chr 5 NC_000005.10:g.132873476_132873479dup
GRCh37.p13 chr 5 NC_000005.9:g.132209168_132209171del
GRCh37.p13 chr 5 NC_000005.9:g.132209168_132209171dup
AFF4 RefSeqGene NG_030340.1:g.95187_95190del
AFF4 RefSeqGene NG_030340.1:g.95187_95190dup
Gene: LEAP2, liver enriched antimicrobial peptide 2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LEAP2 transcript NM_052971.3:c. N/A Upstream Transcript 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18520 TCACTCA=0.86533 TCA=0.13467
European Sub 14152 TCACTCA=0.84243 TCA=0.15757
African Sub 2898 TCACTCA=0.9620 TCA=0.0380
African Others Sub 114 TCACTCA=1.000 TCA=0.000
African American Sub 2784 TCACTCA=0.9605 TCA=0.0395
Asian Sub 112 TCACTCA=0.902 TCA=0.098
East Asian Sub 86 TCACTCA=0.91 TCA=0.09
Other Asian Sub 26 TCACTCA=0.88 TCA=0.12
Latin American 1 Sub 146 TCACTCA=0.925 TCA=0.075
Latin American 2 Sub 610 TCACTCA=0.902 TCA=0.098
South Asian Sub 98 TCACTCA=0.84 TCA=0.16
Other Sub 504 TCACTCA=0.889 TCA=0.111


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 TCACTCA=0.892032 delCTCA=0.107968
gnomAD - Genomes Global Study-wide 140132 TCACTCA=0.888484 delCTCA=0.111516
gnomAD - Genomes European Sub 75872 TCACTCA=0.84404 delCTCA=0.15596
gnomAD - Genomes African Sub 42016 TCACTCA=0.96359 delCTCA=0.03641
gnomAD - Genomes American Sub 13644 TCACTCA=0.90824 delCTCA=0.09176
gnomAD - Genomes Ashkenazi Jewish Sub 3320 TCACTCA=0.8786 delCTCA=0.1214
gnomAD - Genomes East Asian Sub 3130 TCACTCA=0.8792 delCTCA=0.1208
gnomAD - Genomes Other Sub 2150 TCACTCA=0.8926 delCTCA=0.1074
8.3KJPN JAPANESE Study-wide 16760 TCACTCA=0.87524 delCTCA=0.12476
1000Genomes Global Study-wide 5008 TCACTCA=0.8946 delCTCA=0.1054
1000Genomes African Sub 1322 TCACTCA=0.9856 delCTCA=0.0144
1000Genomes East Asian Sub 1008 TCACTCA=0.8849 delCTCA=0.1151
1000Genomes Europe Sub 1006 TCACTCA=0.8549 delCTCA=0.1451
1000Genomes South Asian Sub 978 TCACTCA=0.814 delCTCA=0.186
1000Genomes American Sub 694 TCACTCA=0.906 delCTCA=0.094
Genetic variation in the Estonian population Estonian Study-wide 4480 TCACTCA=0.8489 delCTCA=0.1511
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 TCACTCA=0.8407 delCTCA=0.1593
UK 10K study - Twins TWIN COHORT Study-wide 3708 TCACTCA=0.8433 delCTCA=0.1567
Korean Genome Project KOREAN Study-wide 1832 TCACTCA=0.8635 delCTCA=0.1365
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 TCACTCA=0.805 delCTCA=0.195
Northern Sweden ACPOP Study-wide 600 TCACTCA=0.830 delCTCA=0.170
The Danish reference pan genome Danish Study-wide 40 TCACTCA=0.78 delCTCA=0.23
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 TCACTCA= delCTCA dupCTCA
GRCh38.p13 chr 5 NC_000005.10:g.132873473_132873479= NC_000005.10:g.132873476_132873479del NC_000005.10:g.132873476_132873479dup
GRCh37.p13 chr 5 NC_000005.9:g.132209165_132209171= NC_000005.9:g.132209168_132209171del NC_000005.9:g.132209168_132209171dup
AFF4 RefSeqGene NG_030340.1:g.95184_95190= NG_030340.1:g.95187_95190del NG_030340.1:g.95187_95190dup
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#.

38 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss288659364 May 04, 2012 (137)
2 1000GENOMES ss326721152 May 09, 2011 (134)
3 1000GENOMES ss326765397 May 09, 2011 (134)
4 1000GENOMES ss326992531 May 09, 2011 (134)
5 1000GENOMES ss499275305 May 04, 2012 (137)
6 LUNTER ss551545269 Apr 25, 2013 (138)
7 LUNTER ss551715145 Apr 25, 2013 (138)
8 LUNTER ss553217639 Apr 25, 2013 (138)
9 TISHKOFF ss554221499 Apr 25, 2013 (138)
10 SSMP ss663561605 Apr 01, 2015 (144)
11 WARNICH_LAB ss678323755 Apr 25, 2013 (138)
12 EVA-GONL ss982135670 Aug 21, 2014 (142)
13 1000GENOMES ss1374512013 Aug 21, 2014 (142)
14 DDI ss1536480184 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1576611576 Apr 01, 2015 (144)
16 EVA_DECODE ss1591662917 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1704875214 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1704875304 Apr 01, 2015 (144)
19 HAMMER_LAB ss1804087129 Sep 08, 2015 (146)
20 JJLAB ss2030715515 Sep 14, 2016 (149)
21 TOPMED ss2446551866 Dec 20, 2016 (150)
22 SYSTEMSBIOZJU ss2626139588 Nov 08, 2017 (151)
23 GNOMAD ss2830892559 Nov 08, 2017 (151)
24 SWEGEN ss2997809373 Nov 08, 2017 (151)
25 MCHAISSO ss3066043178 Nov 08, 2017 (151)
26 TOPMED ss3478949911 Nov 08, 2017 (151)
27 BEROUKHIMLAB ss3644195657 Oct 12, 2018 (152)
28 BIOINF_KMB_FNS_UNIBA ss3645908347 Oct 12, 2018 (152)
29 EGCUT_WGS ss3665723235 Jul 13, 2019 (153)
30 EVA_DECODE ss3715721947 Jul 13, 2019 (153)
31 ACPOP ss3732827374 Jul 13, 2019 (153)
32 KHV_HUMAN_GENOMES ss3807249759 Jul 13, 2019 (153)
33 EVA ss3838229906 Apr 26, 2020 (154)
34 EVA ss3843672477 Apr 26, 2020 (154)
35 KOGIC ss3957663532 Apr 26, 2020 (154)
36 EVA ss3986318521 Apr 26, 2021 (155)
37 TOPMED ss4679088415 Apr 26, 2021 (155)
38 TOMMO_GENOMICS ss5174185537 Apr 26, 2021 (155)
39 1000Genomes NC_000005.9 - 132209165 Oct 12, 2018 (152)
40 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 132209165 Oct 12, 2018 (152)
41 Genetic variation in the Estonian population NC_000005.9 - 132209165 Oct 12, 2018 (152)
42 The Danish reference pan genome NC_000005.9 - 132209165 Apr 26, 2020 (154)
43 gnomAD - Genomes NC_000005.10 - 132873473 Apr 26, 2021 (155)
44 Genome of the Netherlands Release 5 NC_000005.9 - 132209165 Apr 26, 2020 (154)
45 Korean Genome Project NC_000005.10 - 132873473 Apr 26, 2020 (154)
46 Northern Sweden NC_000005.9 - 132209165 Jul 13, 2019 (153)
47 8.3KJPN NC_000005.9 - 132209165 Apr 26, 2021 (155)
48 TopMed NC_000005.10 - 132873473 Apr 26, 2021 (155)
49 UK 10K study - Twins NC_000005.9 - 132209165 Oct 12, 2018 (152)
50 ALFA NC_000005.10 - 132873473 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
ss288659364, ss326721152, ss326765397, ss326992531, ss551545269, ss551715145, ss553217639, ss1591662917 NC_000005.8:132237063:TCAC: NC_000005.10:132873472:TCACTCA:TCA (self)
28941213, 16096350, 11461483, 1028641, 7154468, 6112239, 32154844, 16096350, ss499275305, ss663561605, ss678323755, ss982135670, ss1374512013, ss1576611576, ss1704875214, ss1704875304, ss1804087129, ss2030715515, ss2446551866, ss2626139588, ss2830892559, ss2997809373, ss3644195657, ss3665723235, ss3732827374, ss3838229906, ss3986318521, ss5174185537 NC_000005.9:132209164:TCAC: NC_000005.10:132873472:TCACTCA:TCA (self)
ss554221499 NC_000005.9:132209167:CTCA: NC_000005.10:132873472:TCACTCA:TCA (self)
204685812, 14041533, 322953761, 516465972, ss3066043178, ss3478949911, ss3645908347, ss3715721947, ss3807249759, ss3843672477, ss3957663532, ss4679088415 NC_000005.10:132873472:TCAC: NC_000005.10:132873472:TCACTCA:TCA (self)
8391516689 NC_000005.10:132873472:TCACTCA:TCA NC_000005.10:132873472:TCACTCA:TCA (self)
ss1536480184 NC_000005.9:132209164::TCAC NC_000005.10:132873472:TCACTCA:TCA…

NC_000005.10:132873472:TCACTCA:TCACTCACTCA

(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 rs142228782

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.post596+ae089ad