Name: rs149482446
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.

rs149482446

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:22250691 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000064 (16/251304, GnomAD_exome)
T=0.000071 (10/140258, GnomAD)
T=0.000058 (7/121244, ExAC) (+ 8 more)
T=0.00008 (4/48878, ALFA)
T=0.00004 (1/28258, 14KJPN)
T=0.00008 (1/12994, GO-ESP)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EEF2K : Missense 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	65240	C=0.99992	A=0.00000, T=0.00008
European	Sub	47194	C=0.99992	A=0.00000, T=0.00008
African	Sub	8348	C=0.9999	A=0.0000, T=0.0001
African Others	Sub	306	C=1.000	A=0.000, T=0.000
African American	Sub	8042	C=0.9999	A=0.0000, T=0.0001
Asian	Sub	168	C=1.000	A=0.000, T=0.000
East Asian	Sub	112	C=1.000	A=0.000, T=0.000
Other Asian	Sub	56	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	500	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	628	C=1.000	A=0.000, T=0.000
South Asian	Sub	98	C=1.00	A=0.00, T=0.00
Other	Sub	8304	C=1.0000	A=0.0000, T=0.0000

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
gnomAD - Exomes	Global	Study-wide	251304	C=0.999936	T=0.000064
gnomAD - Exomes	European	Sub	135256	C=0.999933	T=0.000067
gnomAD - Exomes	Asian	Sub	49010	C=0.99996	T=0.00004
gnomAD - Exomes	American	Sub	34576	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	16254	C=0.99969	T=0.00031
gnomAD - Exomes	Ashkenazi Jewish	Sub	10070	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6138	C=1.0000	T=0.0000
gnomAD - Genomes	Global	Study-wide	140258	C=0.999929	T=0.000071
gnomAD - Genomes	European	Sub	75960	C=0.99995	T=0.00005
gnomAD - Genomes	African	Sub	42042	C=0.99988	T=0.00012
gnomAD - Genomes	American	Sub	13650	C=0.99993	T=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2150	C=1.0000	T=0.0000
ExAC	Global	Study-wide	121244	C=0.999942	T=0.000058
ExAC	Europe	Sub	73246	C=0.99995	T=0.00005
ExAC	Asian	Sub	25150	C=0.99996	T=0.00004
ExAC	American	Sub	11552	C=1.00000	T=0.00000
ExAC	African	Sub	10398	C=0.99981	T=0.00019
ExAC	Other	Sub	898	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	48878	C=0.99992	A=0.00000, T=0.00008
Allele Frequency Aggregator	European	Sub	37104	C=0.99992	A=0.00000, T=0.00008
Allele Frequency Aggregator	Other	Sub	6870	C=1.0000	A=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	3510	C=0.9997	A=0.0000, T=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	168	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	A=0.00, T=0.00
14KJPN	JAPANESE	Study-wide	28258	C=0.99996	T=0.00004
GO Exome Sequencing Project	Global	Study-wide	12994	C=0.99992	T=0.00008
GO Exome Sequencing Project	European American	Sub	8600	C=1.0000	T=0.0000
GO Exome Sequencing Project	African American	Sub	4394	C=0.9998	T=0.0002
1000Genomes_30x	Global	Study-wide	6404	C=0.9998	T=0.0002
1000Genomes_30x	African	Sub	1786	C=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9998	T=0.0002
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9998	T=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9997	T=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=1.0000	T=0.0000

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 16	NC_000016.10:g.22250691C>A
GRCh38.p14 chr 16	NC_000016.10:g.22250691C>T
GRCh37.p13 chr 16	NC_000016.9:g.22262012C>A
GRCh37.p13 chr 16	NC_000016.9:g.22262012C>T
GRCh38.p14 chr 16 fix patch HG926_PATCH	NW_017852933.1:g.854355G>T
GRCh38.p14 chr 16 fix patch HG926_PATCH	NW_017852933.1:g.854355G>A

Gene: EEF2K, eukaryotic elongation factor 2 kinase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EEF2K transcript	NM_013302.5:c.446C>A	T [ACG] > K [AAG]	Coding Sequence Variant
eukaryotic elongation factor 2 kinase	NP_037434.2:p.Thr149Lys	T (Thr) > K (Lys)	Missense Variant
EEF2K transcript	NM_013302.5:c.446C>T	T [ACG] > M [ATG]	Coding Sequence Variant
eukaryotic elongation factor 2 kinase	NP_037434.2:p.Thr149Met	T (Thr) > M (Met)	Missense 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=	A	T
GRCh38.p14 chr 16	NC_000016.10:g.22250691=	NC_000016.10:g.22250691C>A	NC_000016.10:g.22250691C>T
GRCh37.p13 chr 16	NC_000016.9:g.22262012=	NC_000016.9:g.22262012C>A	NC_000016.9:g.22262012C>T
GRCh38.p14 chr 16 fix patch HG926_PATCH	NW_017852933.1:g.854355=	NW_017852933.1:g.854355G>T	NW_017852933.1:g.854355G>A
EEF2K transcript	NM_013302.5:c.446=	NM_013302.5:c.446C>A	NM_013302.5:c.446C>T
EEF2K transcript	NM_013302.4:c.446=	NM_013302.4:c.446C>A	NM_013302.4:c.446C>T
EEF2K transcript	NM_013302.3:c.446=	NM_013302.3:c.446C>A	NM_013302.3:c.446C>T
eukaryotic elongation factor 2 kinase	NP_037434.2:p.Thr149=	NP_037434.2:p.Thr149Lys	NP_037434.2:p.Thr149Met
eukaryotic elongation factor 2 kinase	NP_037434.1:p.Thr149=	NP_037434.1:p.Thr149Lys	NP_037434.1:p.Thr149Met

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#.

17 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss342423560	May 09, 2011 (134)
2	1000GENOMES	ss1355744274	Aug 21, 2014 (142)
3	EVA_UK10K_ALSPAC	ss1634188430	Apr 01, 2015 (144)
4	EVA_UK10K_TWINSUK	ss1677182463	Apr 01, 2015 (144)
5	EVA_EXAC	ss1692205981	Apr 01, 2015 (144)
6	HUMAN_LONGEVITY	ss2211282379	Dec 20, 2016 (150)
7	GNOMAD	ss2741831863	Nov 08, 2017 (151)
8	GNOMAD	ss2749495977	Nov 08, 2017 (151)
9	GNOMAD	ss2941399799	Nov 08, 2017 (151)
10	ILLUMINA	ss3653835874	Oct 12, 2018 (152)
11	EGCUT_WGS	ss3681319504	Jul 13, 2019 (153)
12	EVA	ss3824997551	Apr 27, 2020 (154)
13	TOPMED	ss5010823603	Apr 27, 2021 (155)
14	TOPMED	ss5010823604	Apr 27, 2021 (155)
15	HUGCELL_USP	ss5493931495	Oct 16, 2022 (156)
16	1000G_HIGH_COVERAGE	ss5602858523	Oct 16, 2022 (156)
17	TOMMO_GENOMICS	ss5773498397	Oct 16, 2022 (156)
18	1000Genomes	NC_000016.9 - 22262012	Oct 12, 2018 (152)
19	1000Genomes_30x	NC_000016.10 - 22250691	Oct 16, 2022 (156)
20	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 22262012	Oct 12, 2018 (152)
21	Genetic variation in the Estonian population	NC_000016.9 - 22262012	Oct 12, 2018 (152)
22	ExAC	NC_000016.9 - 22262012	Oct 12, 2018 (152)
23	gnomAD - Genomes	NC_000016.10 - 22250691	Apr 27, 2021 (155)
24	gnomAD - Exomes	NC_000016.9 - 22262012	Jul 13, 2019 (153)
25	GO Exome Sequencing Project	NC_000016.9 - 22262012	Oct 12, 2018 (152)
26	14KJPN	NC_000016.10 - 22250691	Oct 16, 2022 (156)
27	TopMed Submission ignored due to conflicting rows: Row 226369264 (NC_000016.10:22250690:C:A 2/264690) Row 226369265 (NC_000016.10:22250690:C:T 34/264690)	-	Apr 27, 2021 (155)
28	TopMed Submission ignored due to conflicting rows: Row 226369264 (NC_000016.10:22250690:C:A 2/264690) Row 226369265 (NC_000016.10:22250690:C:T 34/264690)	-	Apr 27, 2021 (155)
29	UK 10K study - Twins	NC_000016.9 - 22262012	Oct 12, 2018 (152)
30	ALFA	NC_000016.10 - 22250691	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
15618589349, ss5010823603	NC_000016.10:22250690:C:A	NC_000016.10:22250690:C:A	(self)
68891001, 38240922, 27057752, 2606577, 11110336, 1454736, 38240922, ss342423560, ss1355744274, ss1634188430, ss1677182463, ss1692205981, ss2741831863, ss2749495977, ss2941399799, ss3653835874, ss3681319504, ss3824997551	NC_000016.9:22262011:C:T	NC_000016.10:22250690:C:T	(self)
90384458, 485519273, 107335501, 15618589349, ss2211282379, ss5010823604, ss5493931495, ss5602858523, ss5773498397	NC_000016.10:22250690:C:T	NC_000016.10:22250690: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 rs149482446

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

rs149482446