Name: rs4445406
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.

rs4445406

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:2607961 (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: T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.415962 (110101/264690, TOPMED)
C=0.409827 (57370/139986, GnomAD)
C=0.49887 (14097/28258, 14KJPN) (+ 15 more)
C=0.37504 (9124/24328, ALFA)
C=0.49570 (8308/16760, 8.3KJPN)
C=0.4942 (3165/6404, 1000G_30x)
C=0.4910 (2459/5008, 1000G)
C=0.3402 (1516/4456, Estonian)
C=0.3531 (1361/3854, ALSPAC)
C=0.3549 (1316/3708, TWINSUK)
C=0.4443 (1301/2928, KOREAN)
C=0.322 (321/998, GoNL)
C=0.398 (239/600, NorthernSweden)
T=0.289 (115/398, SGDP_PRJ)
C=0.431 (93/216, Qatari)
C=0.449 (97/216, Vietnamese)
C=0.28 (11/40, GENOME_DK)
T=0.31 (10/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMEL1 : Intron Variant
Publications: 1 citation
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	24328	T=0.62496	C=0.37504
European	Sub	18110	T=0.66317	C=0.33683
African	Sub	4108	T=0.4722	C=0.5278
African Others	Sub	148	T=0.399	C=0.601
African American	Sub	3960	T=0.4750	C=0.5250
Asian	Sub	124	T=0.444	C=0.556
East Asian	Sub	96	T=0.44	C=0.56
Other Asian	Sub	28	T=0.46	C=0.54
Latin American 1	Sub	168	T=0.607	C=0.393
Latin American 2	Sub	670	T=0.624	C=0.376
South Asian	Sub	98	T=0.49	C=0.51
Other	Sub	1050	T=0.6010	C=0.3990

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	T=0.584038	C=0.415962
gnomAD - Genomes	Global	Study-wide	139986	T=0.590173	C=0.409827
gnomAD - Genomes	European	Sub	75826	T=0.65929	C=0.34071
gnomAD - Genomes	African	Sub	41906	T=0.47709	C=0.52291
gnomAD - Genomes	American	Sub	13646	T=0.55159	C=0.44841
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.6895	C=0.3105
gnomAD - Genomes	East Asian	Sub	3132	T=0.4930	C=0.5070
gnomAD - Genomes	Other	Sub	2152	T=0.5897	C=0.4103
14KJPN	JAPANESE	Study-wide	28258	T=0.50113	C=0.49887
Allele Frequency Aggregator	Total	Global	24328	T=0.62496	C=0.37504
Allele Frequency Aggregator	European	Sub	18110	T=0.66317	C=0.33683
Allele Frequency Aggregator	African	Sub	4108	T=0.4722	C=0.5278
Allele Frequency Aggregator	Other	Sub	1050	T=0.6010	C=0.3990
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.624	C=0.376
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.607	C=0.393
Allele Frequency Aggregator	Asian	Sub	124	T=0.444	C=0.556
Allele Frequency Aggregator	South Asian	Sub	98	T=0.49	C=0.51
8.3KJPN	JAPANESE	Study-wide	16760	T=0.50430	C=0.49570
1000Genomes_30x	Global	Study-wide	6404	T=0.5058	C=0.4942
1000Genomes_30x	African	Sub	1786	T=0.4272	C=0.5728
1000Genomes_30x	Europe	Sub	1266	T=0.6698	C=0.3302
1000Genomes_30x	South Asian	Sub	1202	T=0.4792	C=0.5208
1000Genomes_30x	East Asian	Sub	1170	T=0.4684	C=0.5316
1000Genomes_30x	American	Sub	980	T=0.514	C=0.486
1000Genomes	Global	Study-wide	5008	T=0.5090	C=0.4910
1000Genomes	African	Sub	1322	T=0.4395	C=0.5605
1000Genomes	East Asian	Sub	1008	T=0.4643	C=0.5357
1000Genomes	Europe	Sub	1006	T=0.6710	C=0.3290
1000Genomes	South Asian	Sub	978	T=0.467	C=0.533
1000Genomes	American	Sub	694	T=0.530	C=0.470
Genetic variation in the Estonian population	Estonian	Study-wide	4456	T=0.6598	C=0.3402
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6469	C=0.3531
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6451	C=0.3549
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.5557	C=0.4443, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.678	C=0.322
Northern Sweden	ACPOP	Study-wide	600	T=0.602	C=0.398
SGDP_PRJ	Global	Study-wide	398	T=0.289	C=0.711
Qatari	Global	Study-wide	216	T=0.569	C=0.431
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.551	C=0.449
The Danish reference pan genome	Danish	Study-wide	40	T=0.72	C=0.28
Siberian	Global	Study-wide	32	T=0.31	C=0.69

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.2607961T>C
GRCh38.p14 chr 1	NC_000001.11:g.2607961T>G
GRCh37.p13 chr 1	NC_000001.10:g.2539400T>C
GRCh37.p13 chr 1	NC_000001.10:g.2539400T>G
GRCh38.p14 chr 1 alt locus HSCHR1_1_CTG3	NT_187515.1:g.159151T>C
GRCh38.p14 chr 1 alt locus HSCHR1_1_CTG3	NT_187515.1:g.159151T>G

Gene: MMEL1, membrane metalloendopeptidase like 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MMEL1 transcript	NM_033467.4:c.536-892A>G	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	T=	C	G
GRCh38.p14 chr 1	NC_000001.11:g.2607961=	NC_000001.11:g.2607961T>C	NC_000001.11:g.2607961T>G
GRCh37.p13 chr 1	NC_000001.10:g.2539400=	NC_000001.10:g.2539400T>C	NC_000001.10:g.2539400T>G
GRCh38.p14 chr 1 alt locus HSCHR1_1_CTG3	NT_187515.1:g.159151=	NT_187515.1:g.159151T>C	NT_187515.1:g.159151T>G
MMEL1 transcript	NM_033467.3:c.536-892=	NM_033467.3:c.536-892A>G	NM_033467.3:c.536-892A>C
MMEL1 transcript	NM_033467.4:c.536-892=	NM_033467.4:c.536-892A>G	NM_033467.4:c.536-892A>C
MMEL1 transcript variant X1	XM_005244796.1:c.758-892=	XM_005244796.1:c.758-892A>G	XM_005244796.1:c.758-892A>C

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#.

81 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss5961895	Feb 20, 2003 (111)
2	CSHL-HAPMAP	ss16452249	Feb 27, 2004 (120)
3	ABI	ss41238739	Mar 14, 2006 (126)
4	ILLUMINA	ss74973425	Dec 06, 2007 (129)
5	HGSV	ss85867019	Dec 15, 2007 (130)
6	BGI	ss105113793	Dec 01, 2009 (131)
7	1000GENOMES	ss107942745	Jan 22, 2009 (130)
8	KRIBB_YJKIM	ss119477145	Dec 01, 2009 (131)
9	GMI	ss154545110	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss162994081	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss165996558	Jul 04, 2010 (132)
12	ILLUMINA	ss173734633	Jul 04, 2010 (132)
13	BUSHMAN	ss197908177	Jul 04, 2010 (132)
14	1000GENOMES	ss210452225	Jul 14, 2010 (132)
15	1000GENOMES	ss218197089	Jul 14, 2010 (132)
16	1000GENOMES	ss230400187	Jul 14, 2010 (132)
17	1000GENOMES	ss238119372	Jul 15, 2010 (132)
18	BL	ss252873070	May 09, 2011 (134)
19	GMI	ss275686945	May 04, 2012 (137)
20	GMI	ss283989656	Apr 25, 2013 (138)
21	PJP	ss290496416	May 09, 2011 (134)
22	ILLUMINA	ss537236832	Sep 08, 2015 (146)
23	TISHKOFF	ss553725222	Apr 25, 2013 (138)
24	SSMP	ss647528233	Apr 25, 2013 (138)
25	EVA-GONL	ss974785328	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1067620702	Aug 21, 2014 (142)
27	1000GENOMES	ss1289407627	Aug 21, 2014 (142)
28	DDI	ss1425689531	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1573856343	Apr 01, 2015 (144)
30	EVA_DECODE	ss1584144965	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1599406575	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1642400608	Apr 01, 2015 (144)
33	EVA_SVP	ss1712306179	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1793751493	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1917979257	Feb 12, 2016 (147)
36	GENOMED	ss1966669569	Jul 19, 2016 (147)
37	JJLAB	ss2019506172	Sep 14, 2016 (149)
38	ILLUMINA	ss2094839898	Dec 20, 2016 (150)
39	ILLUMINA	ss2094949468	Dec 20, 2016 (150)
40	USC_VALOUEV	ss2147495041	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2159489472	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624268998	Nov 08, 2017 (151)
43	GRF	ss2697386895	Nov 08, 2017 (151)
44	AFFY	ss2985495518	Nov 08, 2017 (151)
45	SWEGEN	ss2986178863	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023517037	Nov 08, 2017 (151)
47	CSHL	ss3343281709	Nov 08, 2017 (151)
48	ILLUMINA	ss3626009652	Oct 11, 2018 (152)
49	ILLUMINA	ss3637733263	Oct 11, 2018 (152)
50	ILLUMINA	ss3642747493	Oct 11, 2018 (152)
51	ILLUMINA	ss3651368537	Oct 11, 2018 (152)
52	EGCUT_WGS	ss3654286014	Jul 12, 2019 (153)
53	EVA_DECODE	ss3686026831	Jul 12, 2019 (153)
54	ACPOP	ss3726730238	Jul 12, 2019 (153)
55	EVA	ss3745741376	Jul 12, 2019 (153)
56	PACBIO	ss3783306019	Jul 12, 2019 (153)
57	PACBIO	ss3788983461	Jul 12, 2019 (153)
58	PACBIO	ss3793856070	Jul 12, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3798763557	Jul 12, 2019 (153)
60	EVA	ss3825988804	Apr 25, 2020 (154)
61	EVA	ss3836381626	Apr 25, 2020 (154)
62	EVA	ss3841785756	Apr 25, 2020 (154)
63	SGDP_PRJ	ss3848040568	Apr 25, 2020 (154)
64	KRGDB	ss3892889480	Apr 25, 2020 (154)
65	GNOMAD	ss3987197141	Apr 25, 2021 (155)
66	EVA	ss4016889680	Apr 25, 2021 (155)
67	VINODS	ss4019473982	Apr 25, 2021 (155)
68	TOPMED	ss4436984690	Apr 25, 2021 (155)
69	TOMMO_GENOMICS	ss5142140943	Apr 25, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5240926720	Oct 12, 2022 (156)
71	EVA	ss5316294116	Oct 12, 2022 (156)
72	HUGCELL_USP	ss5442161646	Oct 12, 2022 (156)
73	EVA	ss5505750049	Oct 12, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5512578661	Oct 12, 2022 (156)
75	SANFORD_IMAGENETICS	ss5624784004	Oct 12, 2022 (156)
76	TOMMO_GENOMICS	ss5666311814	Oct 12, 2022 (156)
77	YY_MCH	ss5800259501	Oct 12, 2022 (156)
78	EVA	ss5831443513	Oct 12, 2022 (156)
79	EVA	ss5848754859	Oct 12, 2022 (156)
80	EVA	ss5906769092	Oct 12, 2022 (156)
81	EVA	ss5936612700	Oct 12, 2022 (156)
82	1000Genomes	NC_000001.10 - 2539400	Oct 11, 2018 (152)
83	1000Genomes_30x	NC_000001.11 - 2607961	Oct 12, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 2539400	Oct 11, 2018 (152)
85	Genetic variation in the Estonian population	NC_000001.10 - 2539400	Oct 11, 2018 (152)
86	The Danish reference pan genome	NC_000001.10 - 2539400	Apr 25, 2020 (154)
87	gnomAD - Genomes	NC_000001.11 - 2607961	Apr 25, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000001.10 - 2539400	Apr 25, 2020 (154)
89	KOREAN population from KRGDB	NC_000001.10 - 2539400	Apr 25, 2020 (154)
90	Northern Sweden	NC_000001.10 - 2539400	Jul 12, 2019 (153)
91	Qatari	NC_000001.10 - 2539400	Apr 25, 2020 (154)
92	SGDP_PRJ	NC_000001.10 - 2539400	Apr 25, 2020 (154)
93	Siberian	NC_000001.10 - 2539400	Apr 25, 2020 (154)
94	8.3KJPN	NC_000001.10 - 2539400	Apr 25, 2021 (155)
95	14KJPN	NC_000001.11 - 2607961	Oct 12, 2022 (156)
96	TopMed	NC_000001.11 - 2607961	Apr 25, 2021 (155)
97	UK 10K study - Twins	NC_000001.10 - 2539400	Oct 11, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000001.10 - 2539400	Jul 12, 2019 (153)
99	ALFA	NC_000001.11 - 2607961	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)
rs58538957	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85867019	NC_000001.8:2571561:T:C	NC_000001.11:2607960:T:C	(self)
ss107942745, ss162994081, ss165996558, ss197908177, ss210452225, ss252873070, ss275686945, ss283989656, ss290496416, ss1584144965, ss1712306179, ss2094839898, ss3642747493	NC_000001.9:2529259:T:C	NC_000001.11:2607960:T:C	(self)
74504, 31225, 24262, 1363577, 13103, 66874, 15103, 21187, 57548, 11395, 110250, 31225, 6421, ss218197089, ss230400187, ss238119372, ss537236832, ss553725222, ss647528233, ss974785328, ss1067620702, ss1289407627, ss1425689531, ss1573856343, ss1599406575, ss1642400608, ss1793751493, ss1917979257, ss1966669569, ss2019506172, ss2094949468, ss2147495041, ss2624268998, ss2697386895, ss2985495518, ss2986178863, ss3343281709, ss3626009652, ss3637733263, ss3651368537, ss3654286014, ss3726730238, ss3745741376, ss3783306019, ss3788983461, ss3793856070, ss3825988804, ss3836381626, ss3848040568, ss3892889480, ss4016889680, ss5142140943, ss5316294116, ss5505750049, ss5624784004, ss5831443513, ss5936612700	NC_000001.10:2539399:T:C	NC_000001.11:2607960:T:C	(self)
104596, 549532, 148918, 591025, 3982451080, ss2159489472, ss3023517037, ss3686026831, ss3798763557, ss3841785756, ss3987197141, ss4436984690, ss5240926720, ss5442161646, ss5512578661, ss5666311814, ss5800259501, ss5848754859, ss5906769092	NC_000001.11:2607960:T:C	NC_000001.11:2607960:T:C	(self)
ss16452249	NT_004350.16:517061:T:C	NC_000001.11:2607960:T:C	(self)
ss5961895, ss41238739, ss74973425, ss105113793, ss119477145, ss154545110, ss173734633	NT_004350.19:2018031:T:C	NC_000001.11:2607960:T:C	(self)
ss4019473982	NT_187515.1:159150:T:C	NC_000001.11:2607960:T:C	(self)
66874, ss3892889480	NC_000001.10:2539399:T:G	NC_000001.11:2607960:T:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs4445406

PMID	Title	Author	Year	Journal
22057235	Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.	Trynka G et al.	2011	Nature genetics

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

rs4445406