Name: rs35882887
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.

rs35882887

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:171782526 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.180717 (47834/264690, TOPMED)
T=0.187863 (26214/139538, GnomAD)
T=0.06728 (1901/28256, 14KJPN) (+ 16 more)
T=0.19690 (3719/18888, ALFA)
T=0.06826 (1144/16760, 8.3KJPN)
T=0.1724 (1104/6404, 1000G_30x)
T=0.1675 (839/5008, 1000G)
T=0.2396 (1073/4478, Estonian)
T=0.1873 (722/3854, ALSPAC)
T=0.1888 (700/3708, TWINSUK)
T=0.0861 (252/2928, KOREAN)
T=0.0917 (168/1832, Korea1K)
T=0.188 (188/998, GoNL)
T=0.215 (129/600, NorthernSweden)
T=0.162 (35/216, Qatari)
T=0.113 (24/212, Vietnamese)
C=0.468 (72/154, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.46 (11/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: METTL13 : 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	18888	C=0.80310	T=0.19690
European	Sub	14284	C=0.79768	T=0.20232
African	Sub	2946	C=0.8001	T=0.1999
African Others	Sub	114	C=0.842	T=0.158
African American	Sub	2832	C=0.7984	T=0.2016
Asian	Sub	112	C=0.920	T=0.080
East Asian	Sub	86	C=0.93	T=0.07
Other Asian	Sub	26	C=0.88	T=0.12
Latin American 1	Sub	146	C=0.849	T=0.151
Latin American 2	Sub	610	C=0.882	T=0.118
South Asian	Sub	98	C=0.89	T=0.11
Other	Sub	692	C=0.818	T=0.182

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	C=0.819283	T=0.180717
gnomAD - Genomes	Global	Study-wide	139538	C=0.812137	T=0.187863
gnomAD - Genomes	European	Sub	75658	C=0.80474	T=0.19526
gnomAD - Genomes	African	Sub	41682	C=0.80123	T=0.19877
gnomAD - Genomes	American	Sub	13618	C=0.86518	T=0.13482
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	C=0.8249	T=0.1751
gnomAD - Genomes	East Asian	Sub	3122	C=0.8863	T=0.1137
gnomAD - Genomes	Other	Sub	2146	C=0.8206	T=0.1794
14KJPN	JAPANESE	Study-wide	28256	C=0.93272	T=0.06728
Allele Frequency Aggregator	Total	Global	18888	C=0.80310	T=0.19690
Allele Frequency Aggregator	European	Sub	14284	C=0.79768	T=0.20232
Allele Frequency Aggregator	African	Sub	2946	C=0.8001	T=0.1999
Allele Frequency Aggregator	Other	Sub	692	C=0.818	T=0.182
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.882	T=0.118
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.849	T=0.151
Allele Frequency Aggregator	Asian	Sub	112	C=0.920	T=0.080
Allele Frequency Aggregator	South Asian	Sub	98	C=0.89	T=0.11
8.3KJPN	JAPANESE	Study-wide	16760	C=0.93174	T=0.06826
1000Genomes_30x	Global	Study-wide	6404	C=0.8276	T=0.1724
1000Genomes_30x	African	Sub	1786	C=0.7497	T=0.2503
1000Genomes_30x	Europe	Sub	1266	C=0.8065	T=0.1935
1000Genomes_30x	South Asian	Sub	1202	C=0.8993	T=0.1007
1000Genomes_30x	East Asian	Sub	1170	C=0.8581	T=0.1419
1000Genomes_30x	American	Sub	980	C=0.872	T=0.128
1000Genomes	Global	Study-wide	5008	C=0.8325	T=0.1675
1000Genomes	African	Sub	1322	C=0.7564	T=0.2436
1000Genomes	East Asian	Sub	1008	C=0.8671	T=0.1329
1000Genomes	Europe	Sub	1006	C=0.8022	T=0.1978
1000Genomes	South Asian	Sub	978	C=0.896	T=0.104
1000Genomes	American	Sub	694	C=0.882	T=0.118
Genetic variation in the Estonian population	Estonian	Study-wide	4478	C=0.7604	T=0.2396
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8127	T=0.1873
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8112	T=0.1888
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.9139	T=0.0861
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9083	T=0.0917
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.812	T=0.188
Northern Sweden	ACPOP	Study-wide	600	C=0.785	T=0.215
Qatari	Global	Study-wide	216	C=0.838	T=0.162
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.887	T=0.113
SGDP_PRJ	Global	Study-wide	154	C=0.468	T=0.532
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	24	C=0.46	T=0.54

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.171782526C>T
GRCh37.p13 chr 1	NC_000001.10:g.171751666C>T

Gene: METTL13, methyltransferase 13, eEF1A lysine and N-terminal methyltransferase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
METTL13 transcript variant 3	NM_001007239.2:c.153+406C… NM_001007239.2:c.153+406C>T	N/A	Intron Variant
METTL13 transcript variant 2	NM_014955.3:c.-106+731C>T	N/A	Intron Variant
METTL13 transcript variant 1	NM_015935.5:c.153+406C>T	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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.171782526=	NC_000001.11:g.171782526C>T
GRCh37.p13 chr 1	NC_000001.10:g.171751666=	NC_000001.10:g.171751666C>T
EEF1AKNMT transcript variant 3	NM_001007239.1:c.153+406=	NM_001007239.1:c.153+406C>T
METTL13 transcript variant 3	NM_001007239.2:c.153+406=	NM_001007239.2:c.153+406C>T
EEF1AKNMT transcript variant 2	NM_014955.2:c.-106+731=	NM_014955.2:c.-106+731C>T
METTL13 transcript variant 2	NM_014955.3:c.-106+731=	NM_014955.3:c.-106+731C>T
EEF1AKNMT transcript variant 1	NM_015935.4:c.153+406=	NM_015935.4:c.153+406C>T
METTL13 transcript variant 1	NM_015935.5:c.153+406=	NM_015935.5:c.153+406C>T
METTL13 transcript variant X1	XM_005245255.1:c.150+406=	XM_005245255.1:c.150+406C>T
METTL13 transcript variant X2	XM_005245256.1:c.153+406=	XM_005245256.1:c.153+406C>T

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#.

58 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41176388	Mar 15, 2006 (126)
2	BCMHGSC_JDW	ss87868717	Mar 23, 2008 (130)
3	HUMANGENOME_JCVI	ss99261899	Feb 03, 2009 (130)
4	ENSEMBL	ss138104083	Dec 01, 2009 (131)
5	COMPLETE_GENOMICS	ss165433333	Jul 04, 2010 (132)
6	COMPLETE_GENOMICS	ss167277551	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss205503070	Jul 04, 2010 (132)
8	1000GENOMES	ss329027906	May 09, 2011 (134)
9	TISHKOFF	ss554846688	Apr 25, 2013 (138)
10	SSMP	ss648498433	Apr 25, 2013 (138)
11	EVA-GONL	ss975811668	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1068363909	Aug 21, 2014 (142)
13	1000GENOMES	ss1293410653	Aug 21, 2014 (142)
14	DDI	ss1426018087	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1574475844	Apr 01, 2015 (144)
16	EVA_DECODE	ss1585198227	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1601473437	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1644467470	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1795268843	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1919048982	Feb 12, 2016 (147)
21	JJLAB	ss2020040578	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2148068026	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2167516501	Dec 20, 2016 (150)
24	GRF	ss2698046458	Nov 08, 2017 (151)
25	GNOMAD	ss2762678866	Nov 08, 2017 (151)
26	SWEGEN	ss2987949511	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3023779221	Nov 08, 2017 (151)
28	CSHL	ss3343769642	Nov 08, 2017 (151)
29	URBANLAB	ss3646819481	Oct 11, 2018 (152)
30	EGCUT_WGS	ss3655893340	Jul 12, 2019 (153)
31	EVA_DECODE	ss3688020494	Jul 12, 2019 (153)
32	ACPOP	ss3727594038	Jul 12, 2019 (153)
33	EVA	ss3746957553	Jul 12, 2019 (153)
34	PACBIO	ss3783602618	Jul 12, 2019 (153)
35	PACBIO	ss3789228621	Jul 12, 2019 (153)
36	PACBIO	ss3794100684	Jul 12, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3799959413	Jul 12, 2019 (153)
38	EVA	ss3826489697	Apr 25, 2020 (154)
39	EVA	ss3836641812	Apr 25, 2020 (154)
40	EVA	ss3842051824	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3850258166	Apr 25, 2020 (154)
42	KRGDB	ss3895496765	Apr 25, 2020 (154)
43	KOGIC	ss3945892534	Apr 25, 2020 (154)
44	TOPMED	ss4472524221	Apr 25, 2021 (155)
45	TOMMO_GENOMICS	ss5147027939	Apr 25, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5244712427	Oct 13, 2022 (156)
47	EVA	ss5322815772	Oct 13, 2022 (156)
48	HUGCELL_USP	ss5445256804	Oct 13, 2022 (156)
49	EVA	ss5506072751	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5518251161	Oct 13, 2022 (156)
51	SANFORD_IMAGENETICS	ss5626833221	Oct 13, 2022 (156)
52	TOMMO_GENOMICS	ss5674383455	Oct 13, 2022 (156)
53	YY_MCH	ss5801367429	Oct 13, 2022 (156)
54	EVA	ss5832833288	Oct 13, 2022 (156)
55	EVA	ss5849159529	Oct 13, 2022 (156)
56	EVA	ss5910727410	Oct 13, 2022 (156)
57	EVA	ss5938637388	Oct 13, 2022 (156)
58	EVA	ss5979998199	Oct 13, 2022 (156)
59	1000Genomes	NC_000001.10 - 171751666	Oct 11, 2018 (152)
60	1000Genomes_30x	NC_000001.11 - 171782526	Oct 13, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 171751666	Oct 11, 2018 (152)
62	Genetic variation in the Estonian population	NC_000001.10 - 171751666	Oct 11, 2018 (152)
63	The Danish reference pan genome	NC_000001.10 - 171751666	Apr 25, 2020 (154)
64	gnomAD - Genomes	NC_000001.11 - 171782526	Apr 25, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000001.10 - 171751666	Apr 25, 2020 (154)
66	KOREAN population from KRGDB	NC_000001.10 - 171751666	Apr 25, 2020 (154)
67	Korean Genome Project	NC_000001.11 - 171782526	Apr 25, 2020 (154)
68	Northern Sweden	NC_000001.10 - 171751666	Jul 12, 2019 (153)
69	Qatari	NC_000001.10 - 171751666	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000001.10 - 171751666	Apr 25, 2020 (154)
71	Siberian	NC_000001.10 - 171751666	Apr 25, 2020 (154)
72	8.3KJPN	NC_000001.10 - 171751666	Apr 25, 2021 (155)
73	14KJPN	NC_000001.11 - 171782526	Oct 13, 2022 (156)
74	TopMed	NC_000001.11 - 171782526	Apr 25, 2021 (155)
75	UK 10K study - Twins	NC_000001.10 - 171751666	Oct 11, 2018 (152)
76	A Vietnamese Genetic Variation Database	NC_000001.10 - 171751666	Jul 12, 2019 (153)
77	ALFA	NC_000001.11 - 171782526	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)
rs61807974	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87868717, ss165433333, ss167277551, ss205503070, ss1585198227	NC_000001.9:170018288:C:T	NC_000001.11:171782525:C:T	(self)
4219427, 2305734, 1631588, 1759967, 1003603, 2674159, 878903, 1090912, 2275146, 584380, 4997246, 2305734, 496078, ss329027906, ss554846688, ss648498433, ss975811668, ss1068363909, ss1293410653, ss1426018087, ss1574475844, ss1601473437, ss1644467470, ss1795268843, ss1919048982, ss2020040578, ss2148068026, ss2698046458, ss2762678866, ss2987949511, ss3343769642, ss3655893340, ss3727594038, ss3746957553, ss3783602618, ss3789228621, ss3794100684, ss3826489697, ss3836641812, ss3850258166, ss3895496765, ss5147027939, ss5322815772, ss5506072751, ss5626833221, ss5832833288, ss5938637388, ss5979998199	NC_000001.10:171751665:C:T	NC_000001.11:171782525:C:T	(self)
5777096, 30513143, 2270535, 8220559, 36130556, 3782475373, ss2167516501, ss3023779221, ss3646819481, ss3688020494, ss3799959413, ss3842051824, ss3945892534, ss4472524221, ss5244712427, ss5445256804, ss5518251161, ss5674383455, ss5801367429, ss5849159529, ss5910727410	NC_000001.11:171782525:C:T	NC_000001.11:171782525:C:T	(self)
ss41176388, ss99261899, ss138104083	NT_004487.19:23240307:C:T	NC_000001.11:171782525:C:T	(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 rs35882887

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

rs35882887