Name: rs16445
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.

rs16445

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:49903387-49903388 (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: Deletion
Frequency: delCT=0.070362 (18624/264690, TOPMED)
delCT=0.076450 (10718/140196, GnomAD)
delCT=0.092535 (12704/137288, GnomAD_exome) (+ 13 more)
delCT=0.05361 (1515/28258, 14KJPN)
delCT=0.09804 (2697/27508, ALFA)
delCT=0.05394 (904/16760, 8.3KJPN)
delCT=0.11407 (1547/13562, ExAC)
delCT=0.0640 (410/6404, 1000G_30x)
delCT=0.0665 (333/5008, 1000G)
delCT=0.1538 (689/4480, Estonian)
delCT=0.1020 (393/3854, ALSPAC)
delCT=0.1054 (391/3708, TWINSUK)
delCT=0.103 (103/998, GoNL)
delCT=0.147 (88/600, NorthernSweden)
delCT=0.047 (10/214, Vietnamese)
delCT=0.20 (8/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: ALG12 : 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	Alt HMOZ	HTRZ	HWEP
Total	Global	27508	CT=0.90196	=0.09804	0.815036	0.011124	0.17384	3
European	Sub	20214	CT=0.88760	=0.11240	0.788463	0.013258	0.198278	0
African	Sub	3492	CT=0.9679	=0.0321	0.936999	0.001145	0.061856	0
African Others	Sub	122	CT=1.000	=0.000	1.0	0.0	0.0	N/A
African American	Sub	3370	CT=0.9668	=0.0332	0.934718	0.001187	0.064095	0
Asian	Sub	168	CT=0.964	=0.036	0.928571	0.0	0.071429	0
East Asian	Sub	112	CT=0.955	=0.045	0.910714	0.0	0.089286	0
Other Asian	Sub	56	CT=0.98	=0.02	0.964286	0.0	0.035714	0
Latin American 1	Sub	146	CT=0.938	=0.062	0.890411	0.013699	0.09589	1
Latin American 2	Sub	610	CT=0.938	=0.062	0.878689	0.003279	0.118033	0
South Asian	Sub	98	CT=0.95	=0.05	0.897959	0.0	0.102041	0
Other	Sub	2780	CT=0.9083	=0.0917	0.827338	0.010791	0.161871	1

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=0.929638	delCT=0.070362
gnomAD - Genomes	Global	Study-wide	140196	CT=0.923550	delCT=0.076450
gnomAD - Genomes	European	Sub	75908	CT=0.89103	delCT=0.10897
gnomAD - Genomes	African	Sub	42022	CT=0.98091	delCT=0.01909
gnomAD - Genomes	American	Sub	13660	CT=0.92020	delCT=0.07980
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	CT=0.9099	delCT=0.0901
gnomAD - Genomes	East Asian	Sub	3132	CT=0.9658	delCT=0.0342
gnomAD - Genomes	Other	Sub	2154	CT=0.9313	delCT=0.0687
gnomAD - Exomes	Global	Study-wide	137288	CT=0.907465	delCT=0.092535
gnomAD - Exomes	European	Sub	61618	CT=0.89349	delCT=0.10651
gnomAD - Exomes	Asian	Sub	32826	CT=0.90197	delCT=0.09803
gnomAD - Exomes	American	Sub	24150	CT=0.93184	delCT=0.06816
gnomAD - Exomes	Ashkenazi Jewish	Sub	8100	CT=0.8990	delCT=0.1010
gnomAD - Exomes	African	Sub	6444	CT=0.9848	delCT=0.0152
gnomAD - Exomes	Other	Sub	4150	CT=0.9130	delCT=0.0870
14KJPN	JAPANESE	Study-wide	28258	CT=0.94639	delCT=0.05361
Allele Frequency Aggregator	Total	Global	27508	CT=0.90196	delCT=0.09804
Allele Frequency Aggregator	European	Sub	20214	CT=0.88760	delCT=0.11240
Allele Frequency Aggregator	African	Sub	3492	CT=0.9679	delCT=0.0321
Allele Frequency Aggregator	Other	Sub	2780	CT=0.9083	delCT=0.0917
Allele Frequency Aggregator	Latin American 2	Sub	610	CT=0.938	delCT=0.062
Allele Frequency Aggregator	Asian	Sub	168	CT=0.964	delCT=0.036
Allele Frequency Aggregator	Latin American 1	Sub	146	CT=0.938	delCT=0.062
Allele Frequency Aggregator	South Asian	Sub	98	CT=0.95	delCT=0.05
8.3KJPN	JAPANESE	Study-wide	16760	CT=0.94606	delCT=0.05394
ExAC	Global	Study-wide	13562	CT=0.88593	delCT=0.11407
ExAC	Asian	Sub	7472	CT=0.8698	delCT=0.1302
ExAC	Europe	Sub	5170	CT=0.8967	delCT=0.1033
ExAC	African	Sub	564	CT=0.973	delCT=0.027
ExAC	American	Sub	182	CT=0.923	delCT=0.077
ExAC	Other	Sub	174	CT=0.937	delCT=0.063
1000Genomes_30x	Global	Study-wide	6404	CT=0.9360	delCT=0.0640
1000Genomes_30x	African	Sub	1786	CT=0.9961	delCT=0.0039
1000Genomes_30x	Europe	Sub	1266	CT=0.8918	delCT=0.1082
1000Genomes_30x	South Asian	Sub	1202	CT=0.8910	delCT=0.1090
1000Genomes_30x	East Asian	Sub	1170	CT=0.9453	delCT=0.0547
1000Genomes_30x	American	Sub	980	CT=0.928	delCT=0.072
1000Genomes	Global	Study-wide	5008	CT=0.9335	delCT=0.0665
1000Genomes	African	Sub	1322	CT=0.9955	delCT=0.0045
1000Genomes	East Asian	Sub	1008	CT=0.9454	delCT=0.0546
1000Genomes	Europe	Sub	1006	CT=0.8847	delCT=0.1153
1000Genomes	South Asian	Sub	978	CT=0.892	delCT=0.108
1000Genomes	American	Sub	694	CT=0.928	delCT=0.072
Genetic variation in the Estonian population	Estonian	Study-wide	4480	CT=0.8462	delCT=0.1538
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	CT=0.8980	delCT=0.1020
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	CT=0.8946	delCT=0.1054
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	CT=0.897	delCT=0.103
Northern Sweden	ACPOP	Study-wide	600	CT=0.853	delCT=0.147
A Vietnamese Genetic Variation Database	Global	Study-wide	214	CT=0.953	delCT=0.047
The Danish reference pan genome	Danish	Study-wide	40	CT=0.80	delCT=0.20

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 22	NC_000022.11:g.49903387_49903388del
GRCh37.p13 chr 22	NC_000022.10:g.50297035_50297036del
ALG12 RefSeqGene	NG_008927.1:g.20071_20072del

Gene: ALG12, ALG12 alpha-1,6-mannosyltransferase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ALG12 transcript	NM_024105.4:c.450_451=	N/A	3 Prime UTR Variant
ALG12 transcript variant X1	XM_017028936.2:c.1238+791… XM_017028936.2:c.1238+791_1238+792del	N/A	Intron Variant
ALG12 transcript variant X2	XM_017028937.2:c.1238+791… XM_017028937.2:c.1238+791_1238+792del	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.

Allele: delCT (allele ID: 338484 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000322666.3	Congenital disorder of glycosylation	Likely-Benign

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=	delCT
GRCh38.p14 chr 22	NC_000022.11:g.49903387_49903388=	NC_000022.11:g.49903387_49903388del
GRCh37.p13 chr 22	NC_000022.10:g.50297035_50297036=	NC_000022.10:g.50297035_50297036del
ALG12 RefSeqGene	NG_008927.1:g.20071_20072=	NG_008927.1:g.20071_20072del
ALG12 transcript	NM_024105.4:c.450_451=	NM_024105.4:c.450_451del
ALG12 transcript	NM_024105.3:c.450_451=	NM_024105.3:c.450_451del
ALG12 transcript variant X1	XM_017028936.2:c.1238+792=	XM_017028936.2:c.1238+791_1238+792del
ALG12 transcript variant X2	XM_017028937.2:c.1238+792=	XM_017028937.2:c.1238+791_1238+792del

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#.

43 SubSNP, 16 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss103662050	Dec 01, 2009 (131)
2	1000GENOMES	ss328116973	May 09, 2011 (138)
3	1000GENOMES	ss499900637	May 04, 2012 (138)
4	LUNTER	ss552730654	Apr 25, 2013 (138)
5	LUNTER	ss553708279	Apr 25, 2013 (138)
6	SSMP	ss664533399	Apr 01, 2015 (144)
7	EVA-GONL	ss995469055	Aug 21, 2014 (142)
8	1000GENOMES	ss1379165677	Aug 21, 2014 (142)
9	EVA_GENOME_DK	ss1575862852	Apr 01, 2015 (144)
10	EVA_DECODE	ss1699538320	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1709632171	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1709632187	Apr 01, 2015 (144)
13	EVA_EXAC	ss1712256353	Apr 01, 2015 (144)
14	JJLAB	ss2031475184	Sep 14, 2016 (149)
15	GNOMAD	ss2745240549	Nov 08, 2017 (151)
16	GNOMAD	ss2750588274	Nov 08, 2017 (151)
17	GNOMAD	ss2975646406	Nov 08, 2017 (151)
18	SWEGEN	ss3019489491	Nov 08, 2017 (151)
19	BEROUKHIMLAB	ss3644463008	Oct 12, 2018 (152)
20	BIOINF_KMB_FNS_UNIBA	ss3645690550	Oct 12, 2018 (152)
21	EGCUT_WGS	ss3685978185	Jul 13, 2019 (153)
22	EVA_DECODE	ss3708428043	Jul 13, 2019 (153)
23	ACPOP	ss3744033302	Jul 13, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3822682529	Jul 13, 2019 (153)
25	EVA	ss3836050519	Apr 27, 2020 (154)
26	EVA	ss3841653521	Apr 27, 2020 (154)
27	EVA	ss3847169138	Apr 27, 2020 (154)
28	EVA	ss3986870193	Apr 27, 2021 (155)
29	TOPMED	ss5113018440	Apr 27, 2021 (155)
30	TOMMO_GENOMICS	ss5233157879	Apr 27, 2021 (155)
31	EVA	ss5236992842	Apr 27, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5311504866	Oct 16, 2022 (156)
33	HUGCELL_USP	ss5503306213	Oct 16, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5619237180	Oct 16, 2022 (156)
35	EVA	ss5624124227	Oct 16, 2022 (156)
36	SANFORD_IMAGENETICS	ss5664719732	Oct 16, 2022 (156)
37	TOMMO_GENOMICS	ss5794449461	Oct 16, 2022 (156)
38	YY_MCH	ss5818810765	Oct 16, 2022 (156)
39	EVA	ss5822231351	Oct 16, 2022 (156)
40	EVA	ss5848572504	Oct 16, 2022 (156)
41	EVA	ss5853441294	Oct 16, 2022 (156)
42	EVA	ss5882274249	Oct 16, 2022 (156)
43	EVA	ss5959579356	Oct 16, 2022 (156)
44	1000Genomes	NC_000022.10 - 50297035	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000022.11 - 49903387	Oct 16, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 50297035	Oct 12, 2018 (152)
47	Genetic variation in the Estonian population	NC_000022.10 - 50297035	Oct 12, 2018 (152)
48	ExAC	NC_000022.10 - 50297035	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000022.10 - 50297035	Apr 27, 2020 (154)
50	gnomAD - Genomes	NC_000022.11 - 49903387	Apr 27, 2021 (155)
51	gnomAD - Exomes	NC_000022.10 - 50297035	Jul 13, 2019 (153)
52	Genome of the Netherlands Release 5	NC_000022.10 - 50297035	Apr 27, 2020 (154)
53	Northern Sweden	NC_000022.10 - 50297035	Jul 13, 2019 (153)
54	8.3KJPN	NC_000022.10 - 50297035	Apr 27, 2021 (155)
55	14KJPN	NC_000022.11 - 49903387	Oct 16, 2022 (156)
56	TopMed	NC_000022.11 - 49903387	Apr 27, 2021 (155)
57	UK 10K study - Twins	NC_000022.10 - 50297035	Oct 12, 2018 (152)
58	A Vietnamese Genetic Variation Database	NC_000022.10 - 50297035	Jul 13, 2019 (153)
59	ALFA	NC_000022.11 - 49903387	Apr 27, 2021 (155)
60	ClinVar	RCV000322666.3	Oct 16, 2022 (156)

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)
rs146160881	Apr 25, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss328116973, ss552730654, ss553708279, ss1699538320	NC_000022.9:48683038:CT:	NC_000022.11:49903386:CT:	(self)
81181695, 44906622, 31716433, 5997851, 801865, 14575504, 20007423, 17318167, 91127186, 44906622, 9902366, ss499900637, ss664533399, ss995469055, ss1379165677, ss1575862852, ss1709632171, ss1709632187, ss1712256353, ss2031475184, ss2745240549, ss2750588274, ss2975646406, ss3019489491, ss3644463008, ss3685978185, ss3744033302, ss3836050519, ss3841653521, ss3986870193, ss5233157879, ss5624124227, ss5664719732, ss5822231351, ss5848572504, ss5959579356	NC_000022.10:50297034:CT:	NC_000022.11:49903386:CT:	(self)
RCV000322666.3, 106763115, 573147901, 128286565, 388127387, 6610640304, ss3645690550, ss3708428043, ss3822682529, ss3847169138, ss5113018440, ss5236992842, ss5311504866, ss5503306213, ss5619237180, ss5794449461, ss5818810765, ss5853441294, ss5882274249	NC_000022.11:49903386:CT:	NC_000022.11:49903386:CT:	(self)
ss103662050	NT_011520.12:29687603:CT:	NC_000022.11:49903386:CT:	(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 rs16445

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

rs16445