Name: rs1491427680
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.

rs1491427680

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:99264761-99264766 (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=0.003147 (833/264690, TOPMED)
delCT=0.003425 (480/140130, GnomAD)
delCT=0.00394 (73/18520, ALFA) (+ 7 more)
delCT=0.0017 (11/6404, 1000G_30x)
delCT=0.0016 (8/5008, 1000G)
delCT=0.0020 (9/4480, Estonian)
delCT=0.0073 (28/3854, ALSPAC)
delCT=0.0084 (31/3708, TWINSUK)
delCT=0.009 (9/998, GoNL)
delCT=0.002 (1/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LRRC28 : 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	HTRZ	HWEP
Total	Global	18520	CTCTCT=0.99606	CTCT=0.00394	0.992117	0.007883	0
European	Sub	14152	CTCTCT=0.99534	CTCT=0.00466	0.990673	0.009327	0
African	Sub	2898	CTCTCT=0.9986	CTCT=0.0014	0.997239	0.002761	0
African Others	Sub	114	CTCTCT=1.000	CTCT=0.000	1.0	0.0	N/A
African American	Sub	2784	CTCTCT=0.9986	CTCT=0.0014	0.997126	0.002874	0
Asian	Sub	112	CTCTCT=1.000	CTCT=0.000	1.0	0.0	N/A
East Asian	Sub	86	CTCTCT=1.00	CTCT=0.00	1.0	0.0	N/A
Other Asian	Sub	26	CTCTCT=1.00	CTCT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CTCTCT=1.000	CTCT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CTCTCT=0.998	CTCT=0.002	0.996721	0.003279	0
South Asian	Sub	98	CTCTCT=0.99	CTCT=0.01	0.979592	0.020408	0
Other	Sub	504	CTCTCT=0.998	CTCT=0.002	0.996032	0.003968	0

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
TopMed	Global	Study-wide	264690	(CT)₃=0.996853	delCT=0.003147
gnomAD - Genomes	Global	Study-wide	140130	(CT)₃=0.996575	delCT=0.003425
gnomAD - Genomes	European	Sub	75890	(CT)₃=0.99470	delCT=0.00530
gnomAD - Genomes	African	Sub	41992	(CT)₃=0.99905	delCT=0.00095
gnomAD - Genomes	American	Sub	13642	(CT)₃=0.99765	delCT=0.00235
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	(CT)₃=1.0000	delCT=0.0000
gnomAD - Genomes	East Asian	Sub	3130	(CT)₃=1.0000	delCT=0.0000
gnomAD - Genomes	Other	Sub	2152	(CT)₃=0.9972	delCT=0.0028
Allele Frequency Aggregator	Total	Global	18520	(CT)₃=0.99606	delCT=0.00394
Allele Frequency Aggregator	European	Sub	14152	(CT)₃=0.99534	delCT=0.00466
Allele Frequency Aggregator	African	Sub	2898	(CT)₃=0.9986	delCT=0.0014
Allele Frequency Aggregator	Latin American 2	Sub	610	(CT)₃=0.998	delCT=0.002
Allele Frequency Aggregator	Other	Sub	504	(CT)₃=0.998	delCT=0.002
Allele Frequency Aggregator	Latin American 1	Sub	146	(CT)₃=1.000	delCT=0.000
Allele Frequency Aggregator	Asian	Sub	112	(CT)₃=1.000	delCT=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(CT)₃=0.99	delCT=0.01
1000Genomes_30x	Global	Study-wide	6404	(CT)₃=0.9983	delCT=0.0017
1000Genomes_30x	African	Sub	1786	(CT)₃=0.9989	delCT=0.0011
1000Genomes_30x	Europe	Sub	1266	(CT)₃=0.9945	delCT=0.0055
1000Genomes_30x	South Asian	Sub	1202	(CT)₃=1.0000	delCT=0.0000
1000Genomes_30x	East Asian	Sub	1170	(CT)₃=1.0000	delCT=0.0000
1000Genomes_30x	American	Sub	980	(CT)₃=0.998	delCT=0.002
1000Genomes	Global	Study-wide	5008	(CT)₃=0.9984	delCT=0.0016
1000Genomes	African	Sub	1322	(CT)₃=0.9985	delCT=0.0015
1000Genomes	East Asian	Sub	1008	(CT)₃=1.0000	delCT=0.0000
1000Genomes	Europe	Sub	1006	(CT)₃=0.9950	delCT=0.0050
1000Genomes	South Asian	Sub	978	(CT)₃=1.000	delCT=0.000
1000Genomes	American	Sub	694	(CT)₃=0.999	delCT=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4480	(CT)₃=0.9980	delCT=0.0020
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(CT)₃=0.9927	delCT=0.0073
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(CT)₃=0.9916	delCT=0.0084
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	(CT)₃=0.991	delCT=0.009
Northern Sweden	ACPOP	Study-wide	600	(CT)₃=0.998	delCT=0.002

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 15	NC_000015.10:g.99264761CT[2]
GRCh37.p13 chr 15	NC_000015.9:g.99804966CT[2]

Gene: LRRC28, leucine rich repeat containing 28 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC28 transcript variant 2	NM_001284400.3:c.168+8636… NM_001284400.3:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 3	NM_001321675.2:c.168+8636… NM_001321675.2:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 4	NM_001321676.2:c.168+8636… NM_001321676.2:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 5	NM_001321677.2:c.168+8636… NM_001321677.2:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 6	NM_001321678.2:c.33+8788C… NM_001321678.2:c.33+8788CT[2]	N/A	Intron Variant
LRRC28 transcript variant 7	NM_001321679.2:c.-254+863… NM_001321679.2:c.-254+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 8	NM_001321680.2:c.-254+863… NM_001321680.2:c.-254+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 1	NM_144598.5:c.168+8636CT[… NM_144598.5:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant 9	NR_135753.2:n.	N/A	Intron Variant
LRRC28 transcript variant 10	NR_135754.2:n.	N/A	Intron Variant
LRRC28 transcript variant 11	NR_135755.2:n.	N/A	Intron Variant
LRRC28 transcript variant 12	NR_135756.2:n.	N/A	Intron Variant
LRRC28 transcript variant 13	NR_135757.2:n.	N/A	Intron Variant
LRRC28 transcript variant 14	NR_135758.2:n.	N/A	Intron Variant
LRRC28 transcript variant 15	NR_135759.2:n.	N/A	Intron Variant
LRRC28 transcript variant X6	XM_006720389.5:c.168+8636… XM_006720389.5:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X1	XM_011521218.3:c.168+8636… XM_011521218.3:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X2	XM_011521220.3:c.168+8636… XM_011521220.3:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X4	XM_011521221.4:c.168+8636… XM_011521221.4:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X7	XM_017021914.2:c.168+8636… XM_017021914.2:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X3	XM_047432145.1:c.168+8636… XM_047432145.1:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X5	XM_047432146.1:c.168+8636… XM_047432146.1:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X8	XM_047432148.1:c.168+8636… XM_047432148.1:c.168+8636CT[2]	N/A	Intron Variant
LRRC28 transcript variant X9	XM_047432149.1:c.	N/A	Genic Upstream Transcript Variant
LRRC28 transcript variant X10	XM_047432150.1: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	(CT)₃=	delCT
GRCh38.p14 chr 15	NC_000015.10:g.99264761_99264766=	NC_000015.10:g.99264761CT[2]
GRCh37.p13 chr 15	NC_000015.9:g.99804966_99804971=	NC_000015.9:g.99804966CT[2]
LRRC28 transcript variant 2	NM_001284400.3:c.168+8636=	NM_001284400.3:c.168+8636CT[2]
LRRC28 transcript variant 3	NM_001321675.2:c.168+8636=	NM_001321675.2:c.168+8636CT[2]
LRRC28 transcript variant 4	NM_001321676.2:c.168+8636=	NM_001321676.2:c.168+8636CT[2]
LRRC28 transcript variant 5	NM_001321677.2:c.168+8636=	NM_001321677.2:c.168+8636CT[2]
LRRC28 transcript variant 6	NM_001321678.2:c.33+8788=	NM_001321678.2:c.33+8788CT[2]
LRRC28 transcript variant 7	NM_001321679.2:c.-254+8636=	NM_001321679.2:c.-254+8636CT[2]
LRRC28 transcript variant 8	NM_001321680.2:c.-254+8636=	NM_001321680.2:c.-254+8636CT[2]
LRRC28 transcript	NM_144598.2:c.168+8636=	NM_144598.2:c.168+8636CT[2]
LRRC28 transcript variant 1	NM_144598.5:c.168+8636=	NM_144598.5:c.168+8636CT[2]
LRRC28 transcript variant X1	XM_005254859.1:c.168+8636=	XM_005254859.1:c.168+8636CT[2]
LRRC28 transcript variant X2	XM_005254860.1:c.168+8636=	XM_005254860.1:c.168+8636CT[2]
LRRC28 transcript variant X3	XM_005254861.1:c.168+8636=	XM_005254861.1:c.168+8636CT[2]
LRRC28 transcript variant X6	XM_006720389.5:c.168+8636=	XM_006720389.5:c.168+8636CT[2]
LRRC28 transcript variant X1	XM_011521218.3:c.168+8636=	XM_011521218.3:c.168+8636CT[2]
LRRC28 transcript variant X2	XM_011521220.3:c.168+8636=	XM_011521220.3:c.168+8636CT[2]
LRRC28 transcript variant X4	XM_011521221.4:c.168+8636=	XM_011521221.4:c.168+8636CT[2]
LRRC28 transcript variant X7	XM_017021914.2:c.168+8636=	XM_017021914.2:c.168+8636CT[2]
LRRC28 transcript variant X3	XM_047432145.1:c.168+8636=	XM_047432145.1:c.168+8636CT[2]
LRRC28 transcript variant X5	XM_047432146.1:c.168+8636=	XM_047432146.1:c.168+8636CT[2]
LRRC28 transcript variant X8	XM_047432148.1:c.168+8636=	XM_047432148.1:c.168+8636CT[2]

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#.

17 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA-GONL	ss992148157	Jan 10, 2018 (151)
2	1000GENOMES	ss1375384698	Jan 10, 2018 (151)
3	EVA_UK10K_ALSPAC	ss1708428575	Jan 10, 2018 (151)
4	EVA_UK10K_TWINSUK	ss1708428606	Jan 10, 2018 (151)
5	JJLAB	ss2031285954	Jan 10, 2018 (151)
6	GNOMAD	ss2938866726	Jan 10, 2018 (151)
7	SWEGEN	ss3013851802	Jan 10, 2018 (151)
8	EGCUT_WGS	ss3680985799	Jul 13, 2019 (153)
9	EVA_DECODE	ss3698584026	Jul 13, 2019 (153)
10	ACPOP	ss3741224448	Jul 13, 2019 (153)
11	TOPMED	ss5003513565	Apr 27, 2021 (155)
12	1000G_HIGH_COVERAGE	ss5299670727	Oct 17, 2022 (156)
13	HUGCELL_USP	ss5493261454	Oct 17, 2022 (156)
14	1000G_HIGH_COVERAGE	ss5601683951	Oct 17, 2022 (156)
15	EVA	ss5828676612	Oct 17, 2022 (156)
16	EVA	ss5877281166	Oct 17, 2022 (156)
17	EVA	ss5949632062	Oct 17, 2022 (156)
18	1000Genomes	NC_000015.9 - 99804966	Oct 12, 2018 (152)
19	1000Genomes_30x	NC_000015.10 - 99264761	Oct 17, 2022 (156)
20	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 99804966	Oct 12, 2018 (152)
21	Genetic variation in the Estonian population	NC_000015.9 - 99804966	Oct 12, 2018 (152)
22	gnomAD - Genomes	NC_000015.10 - 99264761	Apr 27, 2021 (155)
23	Genome of the Netherlands Release 5	NC_000015.9 - 99804966	Apr 27, 2020 (154)
24	Northern Sweden	NC_000015.9 - 99804966	Jul 13, 2019 (153)
25	TopMed	NC_000015.10 - 99264761	Apr 27, 2021 (155)
26	UK 10K study - Twins	NC_000015.9 - 99804966	Oct 12, 2018 (152)
27	ALFA	NC_000015.10 - 99264761	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
67979528, 37756553, 26724047, 16845702, 14509313, 37756553, ss992148157, ss1375384698, ss1708428575, ss1708428606, ss2031285954, ss2938866726, ss3013851802, ss3680985799, ss3741224448, ss5828676612, ss5949632062	NC_000015.9:99804965:CT:	NC_000015.10:99264760:CTCTCT:CTCT	(self)
89209886, 479189972, 219059225, ss3698584026, ss5003513565, ss5299670727, ss5493261454, ss5601683951, ss5877281166	NC_000015.10:99264760:CT:	NC_000015.10:99264760:CTCTCT:CTCT	(self)
4466258859	NC_000015.10:99264760:CTCTCT:CTCT	NC_000015.10:99264760:CTCTCT:CTCT	(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 rs1491427680

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

rs1491427680