Name: rs143102625
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.

rs143102625

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154756038-154756053 (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: del(GGA)₂ / delGGA / dupGGA
Variation Type: Indel Insertion and Deletion
Frequency: delGGA=0.44283 (8498/19190, 14KJPN)
delGGA=0.45626 (7166/15706, 8.3KJPN)
delGGA=0.31816 (3774/11862, ALFA) (+ 7 more)
delGGA=0.3367 (2156/6404, 1000G_30x)
delGGA=0.3552 (1779/5008, 1000G)
delGGA=0.4172 (1608/3854, ALSPAC)
delGGA=0.4075 (1511/3708, TWINSUK)
delGGA=0.4806 (841/1750, Korea1K)
delGGA=0.434 (252/580, NorthernSweden)
(AGG)₅A=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KCNN3 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	11862	AGGAGGAGGAGGAGGA=0.68184	AGGAGGAGGAGGA=0.31816
European	Sub	7618	AGGAGGAGGAGGAGGA=0.6418	AGGAGGAGGAGGA=0.3582
African	Sub	2816	AGGAGGAGGAGGAGGA=0.8143	AGGAGGAGGAGGA=0.1857
African Others	Sub	108	AGGAGGAGGAGGAGGA=0.833	AGGAGGAGGAGGA=0.167
African American	Sub	2708	AGGAGGAGGAGGAGGA=0.8135	AGGAGGAGGAGGA=0.1865
Asian	Sub	108	AGGAGGAGGAGGAGGA=0.537	AGGAGGAGGAGGA=0.463
East Asian	Sub	84	AGGAGGAGGAGGAGGA=0.56	AGGAGGAGGAGGA=0.44
Other Asian	Sub	24	AGGAGGAGGAGGAGGA=0.46	AGGAGGAGGAGGA=0.54
Latin American 1	Sub	146	AGGAGGAGGAGGAGGA=0.610	AGGAGGAGGAGGA=0.390
Latin American 2	Sub	610	AGGAGGAGGAGGAGGA=0.625	AGGAGGAGGAGGA=0.375
South Asian	Sub	94	AGGAGGAGGAGGAGGA=0.62	AGGAGGAGGAGGA=0.38
Other	Sub	470	AGGAGGAGGAGGAGGA=0.681	AGGAGGAGGAGGA=0.319

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
14KJPN	JAPANESE	Study-wide	19190	(AGG)₅A=0.55717	delGGA=0.44283
8.3KJPN	JAPANESE	Study-wide	15706	(AGG)₅A=0.54374	delGGA=0.45626
Allele Frequency Aggregator	Total	Global	11862	(AGG)₅A=0.68184	delGGA=0.31816
Allele Frequency Aggregator	European	Sub	7618	(AGG)₅A=0.6418	delGGA=0.3582
Allele Frequency Aggregator	African	Sub	2816	(AGG)₅A=0.8143	delGGA=0.1857
Allele Frequency Aggregator	Latin American 2	Sub	610	(AGG)₅A=0.625	delGGA=0.375
Allele Frequency Aggregator	Other	Sub	470	(AGG)₅A=0.681	delGGA=0.319
Allele Frequency Aggregator	Latin American 1	Sub	146	(AGG)₅A=0.610	delGGA=0.390
Allele Frequency Aggregator	Asian	Sub	108	(AGG)₅A=0.537	delGGA=0.463
Allele Frequency Aggregator	South Asian	Sub	94	(AGG)₅A=0.62	delGGA=0.38
1000Genomes_30x	Global	Study-wide	6404	(AGG)₅A=0.6633	delGGA=0.3367
1000Genomes_30x	African	Sub	1786	(AGG)₅A=0.8595	delGGA=0.1405
1000Genomes_30x	Europe	Sub	1266	(AGG)₅A=0.6130	delGGA=0.3870
1000Genomes_30x	South Asian	Sub	1202	(AGG)₅A=0.6481	delGGA=0.3519
1000Genomes_30x	East Asian	Sub	1170	(AGG)₅A=0.5145	delGGA=0.4855
1000Genomes_30x	American	Sub	980	(AGG)₅A=0.567	delGGA=0.433
1000Genomes	Global	Study-wide	5008	(AGG)₅A=0.6448	delGGA=0.3552
1000Genomes	African	Sub	1322	(AGG)₅A=0.8775	delGGA=0.1225
1000Genomes	East Asian	Sub	1008	(AGG)₅A=0.4692	delGGA=0.5308
1000Genomes	Europe	Sub	1006	(AGG)₅A=0.6262	delGGA=0.3738
1000Genomes	South Asian	Sub	978	(AGG)₅A=0.589	delGGA=0.411
1000Genomes	American	Sub	694	(AGG)₅A=0.562	delGGA=0.438
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(AGG)₅A=0.5828	delGGA=0.4172
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(AGG)₅A=0.5925	delGGA=0.4075
Korean Genome Project	KOREAN	Study-wide	1750	(AGG)₅A=0.5194	delGGA=0.4806
Northern Sweden	ACPOP	Study-wide	580	(AGG)₅A=0.566	delGGA=0.434
The Danish reference pan genome	Danish	Study-wide	40	(AGG)₅A=0.38	delGGA=0.62

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 1	NC_000001.11:g.154756039GGA[3]
GRCh38.p14 chr 1	NC_000001.11:g.154756039GGA[4]
GRCh38.p14 chr 1	NC_000001.11:g.154756039GGA[6]
GRCh37.p13 chr 1	NC_000001.10:g.154728515GGA[3]
GRCh37.p13 chr 1	NC_000001.10:g.154728515GGA[4]
GRCh37.p13 chr 1	NC_000001.10:g.154728515GGA[6]
KCNN3 RefSeqGene	NG_016807.2:g.119227CCT[3]
KCNN3 RefSeqGene	NG_016807.2:g.119227CCT[4]
KCNN3 RefSeqGene	NG_016807.2:g.119227CCT[6]

Gene: KCNN3, potassium calcium-activated channel subfamily N member 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KCNN3 transcript variant 3	NM_001204087.2:c.1448+159… NM_001204087.2:c.1448+15923CCT[3]	N/A	Intron Variant
KCNN3 transcript variant 4	NM_001365837.1:c.509+1592… NM_001365837.1:c.509+15923CCT[3]	N/A	Intron Variant
KCNN3 transcript variant 5	NM_001365838.1:c.509+1592… NM_001365838.1:c.509+15923CCT[3]	N/A	Intron Variant
KCNN3 transcript variant 1	NM_002249.6:c.1448+15923C… NM_002249.6:c.1448+15923CCT[3]	N/A	Intron Variant
KCNN3 transcript variant 2	NM_170782.3:c.533+15923CC… NM_170782.3:c.533+15923CCT[3]	N/A	Intron 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	(AGG)₅A=	del(GGA)₂	delGGA	dupGGA
GRCh38.p14 chr 1	NC_000001.11:g.154756038_154756053=	NC_000001.11:g.154756039GGA[3]	NC_000001.11:g.154756039GGA[4]	NC_000001.11:g.154756039GGA[6]
GRCh37.p13 chr 1	NC_000001.10:g.154728514_154728529=	NC_000001.10:g.154728515GGA[3]	NC_000001.10:g.154728515GGA[4]	NC_000001.10:g.154728515GGA[6]
KCNN3 RefSeqGene	NG_016807.2:g.119226_119241=	NG_016807.2:g.119227CCT[3]	NG_016807.2:g.119227CCT[4]	NG_016807.2:g.119227CCT[6]
KCNN3 transcript variant 3	NM_001204087.1:c.1448+15937=	NM_001204087.1:c.1448+15923CCT[3]	NM_001204087.1:c.1448+15923CCT[4]	NM_001204087.1:c.1448+15923CCT[6]
KCNN3 transcript variant 3	NM_001204087.2:c.1448+15937=	NM_001204087.2:c.1448+15923CCT[3]	NM_001204087.2:c.1448+15923CCT[4]	NM_001204087.2:c.1448+15923CCT[6]
KCNN3 transcript variant 4	NM_001365837.1:c.509+15937=	NM_001365837.1:c.509+15923CCT[3]	NM_001365837.1:c.509+15923CCT[4]	NM_001365837.1:c.509+15923CCT[6]
KCNN3 transcript variant 5	NM_001365838.1:c.509+15937=	NM_001365838.1:c.509+15923CCT[3]	NM_001365838.1:c.509+15923CCT[4]	NM_001365838.1:c.509+15923CCT[6]
KCNN3 transcript variant 1	NM_002249.5:c.1448+15937=	NM_002249.5:c.1448+15923CCT[3]	NM_002249.5:c.1448+15923CCT[4]	NM_002249.5:c.1448+15923CCT[6]
KCNN3 transcript variant 1	NM_002249.6:c.1448+15937=	NM_002249.6:c.1448+15923CCT[3]	NM_002249.6:c.1448+15923CCT[4]	NM_002249.6:c.1448+15923CCT[6]
KCNN3 transcript variant 2	NM_170782.2:c.533+15937=	NM_170782.2:c.533+15923CCT[3]	NM_170782.2:c.533+15923CCT[4]	NM_170782.2:c.533+15923CCT[6]
KCNN3 transcript variant 2	NM_170782.3:c.533+15937=	NM_170782.3:c.533+15923CCT[3]	NM_170782.3:c.533+15923CCT[4]	NM_170782.3:c.533+15923CCT[6]
KCNN3 transcript variant X1	XM_005245143.1:c.509+15937=	XM_005245143.1:c.509+15923CCT[3]	XM_005245143.1:c.509+15923CCT[4]	XM_005245143.1:c.509+15923CCT[6]

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#.

53 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss287681214	May 09, 2011 (135)
2	GMI	ss288041701	May 04, 2012 (137)
3	1000GENOMES	ss326086973	May 09, 2011 (134)
4	1000GENOMES	ss326089957	May 09, 2011 (134)
5	1000GENOMES	ss326118249	May 09, 2011 (134)
6	1000GENOMES	ss499001553	May 04, 2012 (137)
7	LUNTER	ss550982206	Apr 25, 2013 (138)
8	LUNTER	ss550999043	Apr 25, 2013 (138)
9	LUNTER	ss552807741	Apr 25, 2013 (138)
10	TISHKOFF	ss553779432	Apr 25, 2013 (138)
11	SSMP	ss663122411	Apr 01, 2015 (144)
12	WARNICH_LAB	ss678270929	Apr 25, 2013 (138)
13	EVA-GONL	ss975683693	Aug 21, 2014 (142)
14	1000GENOMES	ss1367857043	Aug 21, 2014 (142)
15	DDI	ss1536248369	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1574028532	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1701255930	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1701255940	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1795094188	Sep 08, 2015 (146)
20	JJLAB	ss2030349799	Sep 14, 2016 (149)
21	SYSTEMSBIOZJU	ss2624495214	Nov 08, 2017 (151)
22	GNOMAD	ss2761329657	Nov 08, 2017 (151)
23	MCHAISSO	ss3063609317	Nov 08, 2017 (151)
24	MCHAISSO	ss3064425234	Nov 08, 2017 (151)
25	MCHAISSO	ss3065328820	Nov 08, 2017 (151)
26	BEROUKHIMLAB	ss3644069581	Oct 11, 2018 (152)
27	BIOINF_KMB_FNS_UNIBA	ss3645072820	Oct 11, 2018 (152)
28	URBANLAB	ss3646791665	Oct 11, 2018 (152)
29	EVA_DECODE	ss3687784861	Jul 12, 2019 (153)
30	EVA_DECODE	ss3687784862	Jul 12, 2019 (153)
31	EVA_DECODE	ss3687784863	Jul 12, 2019 (153)
32	ACPOP	ss3727486687	Jul 12, 2019 (153)
33	PACBIO	ss3783566691	Jul 12, 2019 (153)
34	PACBIO	ss3789198195	Jul 12, 2019 (153)
35	PACBIO	ss3794070203	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799811078	Jul 12, 2019 (153)
37	EVA	ss3826424738	Apr 25, 2020 (154)
38	EVA	ss3836607025	Apr 25, 2020 (154)
39	EVA	ss3842016255	Apr 25, 2020 (154)
40	KOGIC	ss3945653823	Apr 25, 2020 (154)
41	GNOMAD	ss4003755943	Apr 25, 2021 (155)
42	TOMMO_GENOMICS	ss5146488934	Apr 25, 2021 (155)
43	HUGCELL_USP	ss5444890130	Oct 12, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5517627318	Oct 12, 2022 (156)
45	SANFORD_IMAGENETICS	ss5626593700	Oct 12, 2022 (156)
46	TOMMO_GENOMICS	ss5673686447	Oct 12, 2022 (156)
47	YY_MCH	ss5801261176	Oct 12, 2022 (156)
48	EVA	ss5832667055	Oct 12, 2022 (156)
49	EVA	ss5832667056	Oct 12, 2022 (156)
50	EVA	ss5849109381	Oct 12, 2022 (156)
51	EVA	ss5910250368	Oct 12, 2022 (156)
52	EVA	ss5938387581	Oct 12, 2022 (156)
53	EVA	ss5979990172	Oct 12, 2022 (156)
54	1000Genomes	NC_000001.10 - 154728514	Oct 11, 2018 (152)
55	1000Genomes_30x	NC_000001.11 - 154756038	Oct 12, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154728514	Oct 11, 2018 (152)
57	The Danish reference pan genome	NC_000001.10 - 154728514	Apr 25, 2020 (154)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27086291 (NC_000001.11:154756037:AGG: 32240/90680) Row 27086292 (NC_000001.11:154756037:AGGAGG: 1/91592)	-	Apr 25, 2021 (155)
59	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27086291 (NC_000001.11:154756037:AGG: 32240/90680) Row 27086292 (NC_000001.11:154756037:AGGAGG: 1/91592)	-	Apr 25, 2021 (155)
60	Korean Genome Project	NC_000001.11 - 154756038	Apr 25, 2020 (154)
61	Northern Sweden	NC_000001.10 - 154728514	Jul 12, 2019 (153)
62	8.3KJPN	NC_000001.10 - 154728514	Apr 25, 2021 (155)
63	14KJPN	NC_000001.11 - 154756038	Oct 12, 2022 (156)
64	UK 10K study - Twins	NC_000001.10 - 154728514	Oct 11, 2018 (152)
65	ALFA	NC_000001.11 - 154756038	Apr 25, 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).

Associated ID	History Updated (Build)
rs145395668	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3687784863, ss4003755943	NC_000001.11:154756037:AGGAGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGA	(self)
ss288041701, ss326086973, ss326089957, ss326118249, ss550982206, ss550999043, ss552807741	NC_000001.9:152995137:AGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
3722474, 2023966, 173555, 771552, 4458241, 2023966, ss499001553, ss663122411, ss678270929, ss975683693, ss1367857043, ss1536248369, ss1574028532, ss1701255930, ss1701255940, ss1795094188, ss2030349799, ss2624495214, ss2761329657, ss3644069581, ss3727486687, ss3783566691, ss3789198195, ss3794070203, ss3826424738, ss3836607025, ss5146488934, ss5626593700, ss5832667055, ss5938387581, ss5979990172	NC_000001.10:154728513:AGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
ss553779432	NC_000001.10:154728526:GGA:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
5153253, 2031824, 7523551, ss3063609317, ss3064425234, ss3065328820, ss3645072820, ss3646791665, ss3799811078, ss3842016255, ss3945653823, ss5444890130, ss5517627318, ss5673686447, ss5801261176, ss5849109381, ss5910250368	NC_000001.11:154756037:AGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
3350349351	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
ss3687784862	NC_000001.11:154756040:AGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
ss287681214	NT_004487.19:6217155:AGG:	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGA	(self)
ss5832667056	NC_000001.10:154728513::AGG	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGAGGAGGA
ss3687784861	NC_000001.11:154756043::AGG	NC_000001.11:154756037:AGGAGGAGGAG… NC_000001.11:154756037:AGGAGGAGGAGGAGGA:AGGAGGAGGAGGAGGAGGA	(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 rs143102625

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

rs143102625