Name: rs368353026
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.

rs368353026

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:74880297 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000026 (7/264690, TOPMED)
A=0.000029 (4/140270, GnomAD)
T=0.00004 (1/28258, 14KJPN) (+ 3 more)
A=0.00013 (3/23038, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
A=0.00008 (1/13006, GO-ESP)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HK2 : 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	23038	G=0.99987	A=0.00013
European	Sub	15752	G=0.99987	A=0.00013
African	Sub	3492	G=1.0000	A=0.0000
African Others	Sub	122	G=1.000	A=0.000
African American	Sub	3370	G=1.0000	A=0.0000
Asian	Sub	168	G=1.000	A=0.000
East Asian	Sub	112	G=1.000	A=0.000
Other Asian	Sub	56	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=1.000	A=0.000
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	2772	G=0.9996	A=0.0004

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	G=0.999974	A=0.000026
gnomAD - Genomes	Global	Study-wide	140270	G=0.999971	A=0.000029
gnomAD - Genomes	European	Sub	75946	G=0.99997	A=0.00003
gnomAD - Genomes	African	Sub	42052	G=0.99995	A=0.00005
gnomAD - Genomes	American	Sub	13660	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2154	G=1.0000	A=0.0000
14KJPN	JAPANESE	Study-wide	28258	G=0.99996	T=0.00004
Allele Frequency Aggregator	Total	Global	23038	G=0.99987	A=0.00013
Allele Frequency Aggregator	European	Sub	15752	G=0.99987	A=0.00013
Allele Frequency Aggregator	African	Sub	3492	G=1.0000	A=0.0000
Allele Frequency Aggregator	Other	Sub	2772	G=0.9996	A=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99994	T=0.00006
GO Exome Sequencing Project	Global	Study-wide	13006	G=0.99992	A=0.00008
GO Exome Sequencing Project	European American	Sub	8600	G=0.9999	A=0.0001
GO Exome Sequencing Project	African American	Sub	4406	G=1.0000	A=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 2	NC_000002.12:g.74880297G>A
GRCh38.p14 chr 2	NC_000002.12:g.74880297G>T
GRCh37.p13 chr 2	NC_000002.11:g.75107424G>A
GRCh37.p13 chr 2	NC_000002.11:g.75107424G>T

Gene: HK2, hexokinase 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HK2 transcript variant 1	NM_000189.5:c.1298G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform 1	NP_000180.2:p.Arg433Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant 1	NM_000189.5:c.1298G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform 1	NP_000180.2:p.Arg433Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant 2	NM_001371525.1:c.1214G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform 2	NP_001358454.1:p.Arg405Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant 2	NM_001371525.1:c.1214G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform 2	NP_001358454.1:p.Arg405Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant X1	XM_005264280.3:c.1298G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform X1	XP_005264337.1:p.Arg433Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant X1	XM_005264280.3:c.1298G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform X1	XP_005264337.1:p.Arg433Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant X2	XM_047444084.1:c.1214G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform X2	XP_047300040.1:p.Arg405Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant X2	XM_047444084.1:c.1214G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform X2	XP_047300040.1:p.Arg405Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant X3	XM_047444085.1:c.1214G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform X2	XP_047300041.1:p.Arg405Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant X3	XM_047444085.1:c.1214G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform X2	XP_047300041.1:p.Arg405Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant X4	XM_011532807.3:c.1202G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform X3	XP_011531109.1:p.Arg401Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant X4	XM_011532807.3:c.1202G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform X3	XP_011531109.1:p.Arg401Leu	R (Arg) > L (Leu)	Missense Variant
HK2 transcript variant X5	XM_017003945.3:c.1202G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
hexokinase-2 isoform X4	XP_016859434.1:p.Arg401Gln	R (Arg) > Q (Gln)	Missense Variant
HK2 transcript variant X5	XM_017003945.3:c.1202G>T	R [CGG] > L [CTG]	Coding Sequence Variant
hexokinase-2 isoform X4	XP_016859434.1:p.Arg401Leu	R (Arg) > L (Leu)	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	G=	A	T
GRCh38.p14 chr 2	NC_000002.12:g.74880297=	NC_000002.12:g.74880297G>A	NC_000002.12:g.74880297G>T
GRCh37.p13 chr 2	NC_000002.11:g.75107424=	NC_000002.11:g.75107424G>A	NC_000002.11:g.75107424G>T
HK2 transcript variant 1	NM_000189.5:c.1298=	NM_000189.5:c.1298G>A	NM_000189.5:c.1298G>T
HK2 transcript	NM_000189.4:c.1298=	NM_000189.4:c.1298G>A	NM_000189.4:c.1298G>T
HK2 transcript variant X1	XM_005264280.3:c.1298=	XM_005264280.3:c.1298G>A	XM_005264280.3:c.1298G>T
HK2 transcript variant X1	XM_005264280.2:c.1298=	XM_005264280.2:c.1298G>A	XM_005264280.2:c.1298G>T
HK2 transcript variant X1	XM_005264280.1:c.1298=	XM_005264280.1:c.1298G>A	XM_005264280.1:c.1298G>T
HK2 transcript variant X4	XM_011532807.3:c.1202=	XM_011532807.3:c.1202G>A	XM_011532807.3:c.1202G>T
HK2 transcript variant X2	XM_011532807.2:c.1202=	XM_011532807.2:c.1202G>A	XM_011532807.2:c.1202G>T
HK2 transcript variant X2	XM_011532807.1:c.1202=	XM_011532807.1:c.1202G>A	XM_011532807.1:c.1202G>T
HK2 transcript variant X5	XM_017003945.3:c.1202=	XM_017003945.3:c.1202G>A	XM_017003945.3:c.1202G>T
HK2 transcript variant X3	XM_017003945.2:c.1202=	XM_017003945.2:c.1202G>A	XM_017003945.2:c.1202G>T
HK2 transcript variant X3	XM_017003945.1:c.1202=	XM_017003945.1:c.1202G>A	XM_017003945.1:c.1202G>T
HK2 transcript variant X3	XM_047444085.1:c.1214=	XM_047444085.1:c.1214G>A	XM_047444085.1:c.1214G>T
HK2 transcript variant X2	XM_047444084.1:c.1214=	XM_047444084.1:c.1214G>A	XM_047444084.1:c.1214G>T
HK2 transcript variant 2	NM_001371525.1:c.1214=	NM_001371525.1:c.1214G>A	NM_001371525.1:c.1214G>T
hexokinase-2 isoform 1	NP_000180.2:p.Arg433=	NP_000180.2:p.Arg433Gln	NP_000180.2:p.Arg433Leu
hexokinase-2 isoform X1	XP_005264337.1:p.Arg433=	XP_005264337.1:p.Arg433Gln	XP_005264337.1:p.Arg433Leu
hexokinase-2 isoform X3	XP_011531109.1:p.Arg401=	XP_011531109.1:p.Arg401Gln	XP_011531109.1:p.Arg401Leu
hexokinase-2 isoform X4	XP_016859434.1:p.Arg401=	XP_016859434.1:p.Arg401Gln	XP_016859434.1:p.Arg401Leu
hexokinase-2 isoform X2	XP_047300041.1:p.Arg405=	XP_047300041.1:p.Arg405Gln	XP_047300041.1:p.Arg405Leu
hexokinase-2 isoform X2	XP_047300040.1:p.Arg405=	XP_047300040.1:p.Arg405Gln	XP_047300040.1:p.Arg405Leu
hexokinase-2 isoform 2	NP_001358454.1:p.Arg405=	NP_001358454.1:p.Arg405Gln	NP_001358454.1:p.Arg405Leu

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#.

9 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss712431076	Apr 25, 2013 (138)
2	EVA_EXAC	ss1686377935	Apr 01, 2015 (144)
3	EVA_EXAC	ss1686377936	Apr 01, 2015 (144)
4	GNOMAD	ss2732774115	Nov 08, 2017 (151)
5	EVA	ss3823784180	Apr 25, 2020 (154)
6	GNOMAD	ss4044140547	Apr 26, 2021 (155)
7	TOPMED	ss4511428857	Apr 26, 2021 (155)
8	TOMMO_GENOMICS	ss5152087446	Apr 26, 2021 (155)
9	TOMMO_GENOMICS	ss5680922475	Oct 12, 2022 (156)
10	ExAC Submission ignored due to conflicting rows: Row 6253953 (NC_000002.11:75107423:G:G 120320/120324, NC_000002.11:75107423:G:A 4/120324) Row 6253954 (NC_000002.11:75107423:G:G 120323/120324, NC_000002.11:75107423:G:T 1/120324)	-	Oct 11, 2018 (152)
11	ExAC Submission ignored due to conflicting rows: Row 6253953 (NC_000002.11:75107423:G:G 120320/120324, NC_000002.11:75107423:G:A 4/120324) Row 6253954 (NC_000002.11:75107423:G:G 120323/120324, NC_000002.11:75107423:G:T 1/120324)	-	Oct 11, 2018 (152)
12	gnomAD - Genomes	NC_000002.12 - 74880297	Apr 26, 2021 (155)
13	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1827644 (NC_000002.11:75107423:G:G 250799/250806, NC_000002.11:75107423:G:A 7/250806) Row 1827645 (NC_000002.11:75107423:G:G 250805/250806, NC_000002.11:75107423:G:T 1/250806)	-	Jul 13, 2019 (153)
14	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1827644 (NC_000002.11:75107423:G:G 250799/250806, NC_000002.11:75107423:G:A 7/250806) Row 1827645 (NC_000002.11:75107423:G:G 250805/250806, NC_000002.11:75107423:G:T 1/250806)	-	Jul 13, 2019 (153)
15	GO Exome Sequencing Project	NC_000002.11 - 75107424	Oct 11, 2018 (152)
16	8.3KJPN	NC_000002.11 - 75107424	Apr 26, 2021 (155)
17	14KJPN	NC_000002.12 - 74880297	Oct 12, 2022 (156)
18	TopMed	NC_000002.12 - 74880297	Apr 26, 2021 (155)
19	ALFA	NC_000002.12 - 74880297	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
242634, ss712431076, ss1686377936, ss2732774115, ss3823784180	NC_000002.11:75107423:G:A	NC_000002.12:74880296:G:A	(self)
62854123, 315251736, 7708093893, ss4044140547, ss4511428857	NC_000002.12:74880296:G:A	NC_000002.12:74880296:G:A	(self)
10056753, ss1686377935, ss2732774115, ss5152087446	NC_000002.11:75107423:G:T	NC_000002.12:74880296:G:T	(self)
14759579, ss5680922475	NC_000002.12:74880296:G:T	NC_000002.12:74880296:G:T

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

No publications for rs368353026

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

rs368353026