Name: rs10617728
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.

rs10617728

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:102627026-102627038 (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: delAATG
Variation Type: Indel Insertion and Deletion
Frequency: (GAAT)₃G=0.270127 (71500/264690, TOPMED)
(GAAT)₃G=0.271414 (37846/139440, GnomAD)
(GAAT)₃G=0.08996 (2542/28258, 14KJPN) (+ 9 more)
(GAAT)₃G=0.26033 (4821/18519, ALFA)
(GAAT)₃G=0.09160 (1535/16758, 8.3KJPN)
(GAAT)₃G=0.3047 (1526/5008, 1000G)
(GAAT)₃G=0.2477 (1109/4478, Estonian)
(GAAT)₃G=0.2250 (867/3854, ALSPAC)
(GAAT)₃G=0.2198 (815/3708, TWINSUK)
(GAAT)₃G=0.1037 (190/1832, Korea1K)
(GAAT)₃G=0.243 (146/600, NorthernSweden)
(GAAT)₃G=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMP20 : 2KB Upstream Variant
LOC101928477 : 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	18519	GAATGAATGAATG=0.26033	GAATGAATG=0.73967
European	Sub	14151	GAATGAATGAATG=0.23737	GAATGAATG=0.76263
African	Sub	2898	GAATGAATGAATG=0.3734	GAATGAATG=0.6266
African Others	Sub	114	GAATGAATGAATG=0.439	GAATGAATG=0.561
African American	Sub	2784	GAATGAATGAATG=0.3707	GAATGAATG=0.6293
Asian	Sub	112	GAATGAATGAATG=0.080	GAATGAATG=0.920
East Asian	Sub	86	GAATGAATGAATG=0.10	GAATGAATG=0.90
Other Asian	Sub	26	GAATGAATGAATG=0.00	GAATGAATG=1.00
Latin American 1	Sub	146	GAATGAATGAATG=0.260	GAATGAATG=0.740
Latin American 2	Sub	610	GAATGAATGAATG=0.269	GAATGAATG=0.731
South Asian	Sub	98	GAATGAATGAATG=0.17	GAATGAATG=0.83
Other	Sub	504	GAATGAATGAATG=0.302	GAATGAATG=0.698

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	(GAAT)₃G=0.270127	delAATG=0.729873
gnomAD - Genomes	Global	Study-wide	139440	(GAAT)₃G=0.271414	delAATG=0.728586
gnomAD - Genomes	European	Sub	75570	(GAAT)₃G=0.22602	delAATG=0.77398
gnomAD - Genomes	African	Sub	41716	(GAAT)₃G=0.37206	delAATG=0.62794
gnomAD - Genomes	American	Sub	13580	(GAAT)₃G=0.25022	delAATG=0.74978
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	(GAAT)₃G=0.3116	delAATG=0.6884
gnomAD - Genomes	East Asian	Sub	3120	(GAAT)₃G=0.0830	delAATG=0.9170
gnomAD - Genomes	Other	Sub	2142	(GAAT)₃G=0.2596	delAATG=0.7404
14KJPN	JAPANESE	Study-wide	28258	(GAAT)₃G=0.08996	delAATG=0.91004
Allele Frequency Aggregator	Total	Global	18519	(GAAT)₃G=0.26033	delAATG=0.73967
Allele Frequency Aggregator	European	Sub	14151	(GAAT)₃G=0.23737	delAATG=0.76263
Allele Frequency Aggregator	African	Sub	2898	(GAAT)₃G=0.3734	delAATG=0.6266
Allele Frequency Aggregator	Latin American 2	Sub	610	(GAAT)₃G=0.269	delAATG=0.731
Allele Frequency Aggregator	Other	Sub	504	(GAAT)₃G=0.302	delAATG=0.698
Allele Frequency Aggregator	Latin American 1	Sub	146	(GAAT)₃G=0.260	delAATG=0.740
Allele Frequency Aggregator	Asian	Sub	112	(GAAT)₃G=0.080	delAATG=0.920
Allele Frequency Aggregator	South Asian	Sub	98	(GAAT)₃G=0.17	delAATG=0.83
8.3KJPN	JAPANESE	Study-wide	16758	(GAAT)₃G=0.09160	delAATG=0.90840
1000Genomes	Global	Study-wide	5008	(GAAT)₃G=0.3047	delAATG=0.6953
1000Genomes	African	Sub	1322	(GAAT)₃G=0.4274	delAATG=0.5726
1000Genomes	East Asian	Sub	1008	(GAAT)₃G=0.1687	delAATG=0.8313
1000Genomes	Europe	Sub	1006	(GAAT)₃G=0.2972	delAATG=0.7028
1000Genomes	South Asian	Sub	978	(GAAT)₃G=0.282	delAATG=0.718
1000Genomes	American	Sub	694	(GAAT)₃G=0.311	delAATG=0.689
Genetic variation in the Estonian population	Estonian	Study-wide	4478	(GAAT)₃G=0.2477	delAATG=0.7523
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(GAAT)₃G=0.2250	delAATG=0.7750
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(GAAT)₃G=0.2198	delAATG=0.7802
Korean Genome Project	KOREAN	Study-wide	1832	(GAAT)₃G=0.1037	delAATG=0.8963
Northern Sweden	ACPOP	Study-wide	600	(GAAT)₃G=0.243	delAATG=0.757
The Danish reference pan genome	Danish	Study-wide	40	(GAAT)₃G=0.33	delAATG=0.68

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 11	NC_000011.10:g.102627027AATG[2]
GRCh37.p13 chr 11	NC_000011.9:g.102497758AATG[2]
MMP20 RefSeqGene	NG_012151.1:g.3296ATTC[2]

Gene: MMP20, matrix metallopeptidase 20 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MMP20 transcript	NM_004771.4:c.	N/A	Upstream Transcript Variant

Gene: LOC101928477, uncharacterized LOC101928477 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928477 transcript variant X4	XR_001748340.2:n.	N/A	Intron Variant
LOC101928477 transcript variant X3	XR_947958.3:n.	N/A	Intron Variant
LOC101928477 transcript variant X5	XR_001748341.2:n.	N/A	Genic Upstream Transcript Variant
LOC101928477 transcript variant X2	XR_007062866.1:n.	N/A	Genic Upstream Transcript Variant
LOC101928477 transcript variant X6	XR_007062867.1:n.	N/A	Genic Upstream Transcript Variant
LOC101928477 transcript variant X1	XR_947957.3:n.	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	(GAAT)₃G=	delAATG
GRCh38.p14 chr 11	NC_000011.10:g.102627026_102627038=	NC_000011.10:g.102627027AATG[2]
GRCh37.p13 chr 11	NC_000011.9:g.102497757_102497769=	NC_000011.9:g.102497758AATG[2]
MMP20 RefSeqGene	NG_012151.1:g.3295_3307=	NG_012151.1:g.3296ATTC[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#.

54 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77858588	Dec 06, 2007 (129)
2	HGSV	ss77864834	Dec 06, 2007 (129)
3	HGSV	ss77952332	Dec 06, 2007 (129)
4	HUMANGENOME_JCVI	ss97438737	Feb 05, 2009 (130)
5	BUSHMAN	ss193247957	Jul 04, 2010 (138)
6	GMI	ss287881022	May 09, 2011 (138)
7	GMI	ss289092560	May 04, 2012 (138)
8	PJP	ss294719770	May 09, 2011 (138)
9	PJP	ss294719771	May 09, 2011 (135)
10	1000GENOMES	ss327373801	May 09, 2011 (138)
11	1000GENOMES	ss327463426	May 09, 2011 (138)
12	1000GENOMES	ss327885237	May 09, 2011 (138)
13	LUNTER	ss552159641	Apr 25, 2013 (138)
14	LUNTER	ss552424219	Apr 25, 2013 (138)
15	LUNTER	ss553462552	Apr 25, 2013 (138)
16	SSMP	ss664017457	Apr 01, 2015 (144)
17	BILGI_BIOE	ss666547520	Apr 25, 2013 (138)
18	1000GENOMES	ss1371433732	Aug 21, 2014 (142)
19	DDI	ss1536703789	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1574407104	Apr 01, 2015 (144)
21	EVA_DECODE	ss1598562920	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1707233634	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1707233644	Apr 01, 2015 (144)
24	JJLAB	ss2031096978	Sep 14, 2016 (149)
25	SYSTEMSBIOZJU	ss2627910733	Nov 08, 2017 (151)
26	SWEGEN	ss3008684287	Nov 08, 2017 (151)
27	MCHAISSO	ss3063705270	Nov 08, 2017 (151)
28	MCHAISSO	ss3064531573	Nov 08, 2017 (151)
29	MCHAISSO	ss3065445983	Nov 08, 2017 (151)
30	BEROUKHIMLAB	ss3644327684	Oct 12, 2018 (152)
31	BIOINF_KMB_FNS_UNIBA	ss3645216840	Oct 12, 2018 (152)
32	URBANLAB	ss3649690773	Oct 12, 2018 (152)
33	EGCUT_WGS	ss3676005906	Jul 13, 2019 (153)
34	EVA_DECODE	ss3692482387	Jul 13, 2019 (153)
35	ACPOP	ss3738488771	Jul 13, 2019 (153)
36	PACBIO	ss3787051008	Jul 13, 2019 (153)
37	PACBIO	ss3792177847	Jul 13, 2019 (153)
38	PACBIO	ss3797060345	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3815070093	Jul 13, 2019 (153)
40	EVA	ss3832808346	Apr 26, 2020 (154)
41	EVA	ss3839965778	Apr 26, 2020 (154)
42	EVA	ss3845446969	Apr 26, 2020 (154)
43	KOGIC	ss3970631501	Apr 26, 2020 (154)
44	GNOMAD	ss4241437722	Apr 26, 2021 (155)
45	TOPMED	ss4897827921	Apr 26, 2021 (155)
46	TOMMO_GENOMICS	ss5203620572	Apr 26, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5288692221	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5483701897	Oct 16, 2022 (156)
49	TOMMO_GENOMICS	ss5751991060	Oct 16, 2022 (156)
50	YY_MCH	ss5812726060	Oct 16, 2022 (156)
51	EVA	ss5837146268	Oct 16, 2022 (156)
52	EVA	ss5850125278	Oct 16, 2022 (156)
53	EVA	ss5921412740	Oct 16, 2022 (156)
54	EVA	ss5943275370	Oct 16, 2022 (156)
55	1000Genomes	NC_000011.9 - 102497757	Oct 12, 2018 (152)
56	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 102497757	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000011.9 - 102497757	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000011.9 - 102497757	Apr 26, 2020 (154)
59	gnomAD - Genomes	NC_000011.10 - 102627026	Apr 26, 2021 (155)
60	Korean Genome Project	NC_000011.10 - 102627026	Apr 26, 2020 (154)
61	Northern Sweden	NC_000011.9 - 102497757	Jul 13, 2019 (153)
62	8.3KJPN	NC_000011.9 - 102497757	Apr 26, 2021 (155)
63	14KJPN	NC_000011.10 - 102627026	Oct 16, 2022 (156)
64	TopMed	NC_000011.10 - 102627026	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000011.9 - 102497757	Oct 12, 2018 (152)
66	ALFA	NC_000011.10 - 102627026	Apr 26, 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)
rs35814478	May 23, 2006 (127)
rs66639816	Apr 25, 2013 (138)
rs66639817	Feb 26, 2009 (130)
rs66639818	Feb 26, 2009 (130)
rs138486044	Sep 17, 2011 (135)
rs138545064	Sep 17, 2011 (135)
rs142792531	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss289092560, ss294719770, ss327373801, ss327463426, ss327885237, ss552159641, ss552424219, ss553462552, ss1598562920	NC_000011.8:102002966:GAAT:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
ss77858588, ss77864834, ss77952332, ss294719771	NC_000011.8:102002975:AATG:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
55296631, 30687310, 21744154, 317172, 11773636, 61589879, 30687310, ss664017457, ss666547520, ss1371433732, ss1536703789, ss1574407104, ss1707233634, ss1707233644, ss2031096978, ss2627910733, ss3008684287, ss3644327684, ss3676005906, ss3738488771, ss3787051008, ss3792177847, ss3797060345, ss3832808346, ss3839965778, ss5203620572, ss5837146268, ss5943275370	NC_000011.9:102497756:GAAT:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
390201613, 27009502, 85828164, 113373577, ss3063705270, ss3064531573, ss3065445983, ss3645216840, ss3649690773, ss3692482387, ss3815070093, ss3845446969, ss3970631501, ss4241437722, ss4897827921, ss5288692221, ss5483701897, ss5751991060, ss5812726060, ss5850125278, ss5921412740	NC_000011.10:102627025:GAAT:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
2573596926	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
ss287881022	NT_033899.8:6060172:GAAT:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
ss97438737	NT_033899.8:6060181:AATG:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(self)
ss193247957	NT_033899.9:14624129:GAAT:	NC_000011.10:102627025:GAATGAATGAA… NC_000011.10:102627025:GAATGAATGAATG:GAATGAATG	(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 rs10617728

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
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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

rs10617728