Name: rs7354830
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.

rs7354830

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:119034693 (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=0.021537 (3019/140176, GnomAD)
C=0.00130 (33/25302, ALFA)
C=0.0264 (169/6404, 1000G_30x) (+ 7 more)
C=0.0260 (130/5008, 1000G)
C=0.0000 (0/3854, ALSPAC)
C=0.0005 (2/3708, TWINSUK)
C=0.002 (2/998, GoNL)
C=0.014 (3/216, Qatari)
T=0.5 (4/8, SGDP_PRJ)
C=0.5 (4/8, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: WARS2 : 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	25302	T=0.99870	C=0.00130, G=0.00000
European	Sub	20266	T=0.99956	C=0.00044, G=0.00000
African	Sub	2768	T=0.9928	C=0.0072, G=0.0000
African Others	Sub	110	T=0.982	C=0.018, G=0.000
African American	Sub	2658	T=0.9932	C=0.0068, G=0.0000
Asian	Sub	128	T=1.000	C=0.000, G=0.000
East Asian	Sub	100	T=1.00	C=0.00, G=0.00
Other Asian	Sub	28	T=1.00	C=0.00, G=0.00
Latin American 1	Sub	162	T=0.994	C=0.006, G=0.000
Latin American 2	Sub	688	T=1.000	C=0.000, G=0.000
South Asian	Sub	114	T=1.000	C=0.000, G=0.000
Other	Sub	1176	T=0.9974	C=0.0026, G=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 - Genomes	Global	Study-wide	140176	T=0.978463	C=0.021537
gnomAD - Genomes	European	Sub	75926	T=0.99945	C=0.00055
gnomAD - Genomes	African	Sub	41990	T=0.93222	C=0.06778
gnomAD - Genomes	American	Sub	13660	T=0.99283	C=0.00717
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3132	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2150	T=0.9847	C=0.0153
Allele Frequency Aggregator	Total	Global	25302	T=0.99870	C=0.00130, G=0.00000
Allele Frequency Aggregator	European	Sub	20266	T=0.99956	C=0.00044, G=0.00000
Allele Frequency Aggregator	African	Sub	2768	T=0.9928	C=0.0072, G=0.0000
Allele Frequency Aggregator	Other	Sub	1176	T=0.9974	C=0.0026, G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	688	T=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	162	T=0.994	C=0.006, G=0.000
Allele Frequency Aggregator	Asian	Sub	128	T=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	114	T=1.000	C=0.000, G=0.000
1000Genomes_30x	Global	Study-wide	6404	T=0.9733	C=0.0264, G=0.0003
1000Genomes_30x	African	Sub	1786	T=0.9099	C=0.0901, G=0.0000
1000Genomes_30x	Europe	Sub	1266	T=1.0000	C=0.0000, G=0.0000
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000, G=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000, G=0.0000
1000Genomes_30x	American	Sub	980	T=0.990	C=0.008, G=0.002
1000Genomes	Global	Study-wide	5008	T=0.9740	C=0.0260
1000Genomes	African	Sub	1322	T=0.9062	C=0.0938
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=0.991	C=0.009
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=1.0000	C=0.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9995	C=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.998	C=0.002
Qatari	Global	Study-wide	216	T=0.986	C=0.014
SGDP_PRJ	Global	Study-wide	8	T=0.5	C=0.5

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.119034693T>C
GRCh38.p14 chr 1	NC_000001.11:g.119034693T>G
GRCh37.p13 chr 1	NC_000001.10:g.119577316T>C
GRCh37.p13 chr 1	NC_000001.10:g.119577316T>G
WARS2 RefSeqGene	NG_050658.1:g.111096A>G
WARS2 RefSeqGene	NG_050658.1:g.111096A>C

Gene: WARS2, tryptophanyl tRNA synthetase 2, mitochondrial (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
WARS2 transcript variant 3	NM_001378226.1:c.447-480A… NM_001378226.1:c.447-480A>G	N/A	Intron Variant
WARS2 transcript variant 4	NM_001378227.1:c.447-480A… NM_001378227.1:c.447-480A>G	N/A	Intron Variant
WARS2 transcript variant 5	NM_001378228.1:c.345-480A… NM_001378228.1:c.345-480A>G	N/A	Intron Variant
WARS2 transcript variant 6	NM_001378229.1:c.258-480A… NM_001378229.1:c.258-480A>G	N/A	Intron Variant
WARS2 transcript variant 7	NM_001378230.1:c.234-480A… NM_001378230.1:c.234-480A>G	N/A	Intron Variant
WARS2 transcript variant 8	NM_001378231.1:c.430-480A… NM_001378231.1:c.430-480A>G	N/A	Intron Variant
WARS2 transcript variant 1	NM_015836.4:c.516-480A>G	N/A	Intron Variant
WARS2 transcript variant 2	NM_201263.2:c.516-480A>G	N/A	Intron Variant
WARS2 transcript variant X1	XM_005270350.4:c.462-480A… XM_005270350.4:c.462-480A>G	N/A	Intron Variant
WARS2 transcript variant X2	XM_017000038.2:c.430-480A… XM_017000038.2:c.430-480A>G	N/A	Intron Variant
WARS2 transcript variant X3	XM_024449826.2:c.447-480A… XM_024449826.2:c.447-480A>G	N/A	Intron Variant
WARS2 transcript variant X5	XM_024449860.2:c.234-480A… XM_024449860.2:c.234-480A>G	N/A	Intron Variant
WARS2 transcript variant X4	XM_047429105.1:c.259-480A… XM_047429105.1:c.259-480A>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.119034693=	NC_000001.11:g.119034693T>C	NC_000001.11:g.119034693T>G
GRCh37.p13 chr 1	NC_000001.10:g.119577316=	NC_000001.10:g.119577316T>C	NC_000001.10:g.119577316T>G
WARS2 RefSeqGene	NG_050658.1:g.111096=	NG_050658.1:g.111096A>G	NG_050658.1:g.111096A>C
WARS2 transcript variant 3	NM_001378226.1:c.447-480=	NM_001378226.1:c.447-480A>G	NM_001378226.1:c.447-480A>C
WARS2 transcript variant 4	NM_001378227.1:c.447-480=	NM_001378227.1:c.447-480A>G	NM_001378227.1:c.447-480A>C
WARS2 transcript variant 5	NM_001378228.1:c.345-480=	NM_001378228.1:c.345-480A>G	NM_001378228.1:c.345-480A>C
WARS2 transcript variant 6	NM_001378229.1:c.258-480=	NM_001378229.1:c.258-480A>G	NM_001378229.1:c.258-480A>C
WARS2 transcript variant 7	NM_001378230.1:c.234-480=	NM_001378230.1:c.234-480A>G	NM_001378230.1:c.234-480A>C
WARS2 transcript variant 8	NM_001378231.1:c.430-480=	NM_001378231.1:c.430-480A>G	NM_001378231.1:c.430-480A>C
WARS2 transcript variant 1	NM_015836.3:c.516-480=	NM_015836.3:c.516-480A>G	NM_015836.3:c.516-480A>C
WARS2 transcript variant 1	NM_015836.4:c.516-480=	NM_015836.4:c.516-480A>G	NM_015836.4:c.516-480A>C
WARS2 transcript variant 2	NM_201263.2:c.516-480=	NM_201263.2:c.516-480A>G	NM_201263.2:c.516-480A>C
WARS2 transcript variant X1	XM_005270350.1:c.462-480=	XM_005270350.1:c.462-480A>G	XM_005270350.1:c.462-480A>C
WARS2 transcript variant X1	XM_005270350.4:c.462-480=	XM_005270350.4:c.462-480A>G	XM_005270350.4:c.462-480A>C
WARS2 transcript variant X2	XM_005270351.1:c.345-480=	XM_005270351.1:c.345-480A>G	XM_005270351.1:c.345-480A>C
WARS2 transcript variant X3	XM_005270352.1:c.430-480=	XM_005270352.1:c.430-480A>G	XM_005270352.1:c.430-480A>C
WARS2 transcript variant X2	XM_017000038.2:c.430-480=	XM_017000038.2:c.430-480A>G	XM_017000038.2:c.430-480A>C
WARS2 transcript variant X3	XM_024449826.2:c.447-480=	XM_024449826.2:c.447-480A>G	XM_024449826.2:c.447-480A>C
WARS2 transcript variant X5	XM_024449860.2:c.234-480=	XM_024449860.2:c.234-480A>G	XM_024449860.2:c.234-480A>C
WARS2 transcript variant X4	XM_047429105.1:c.259-480=	XM_047429105.1:c.259-480A>G	XM_047429105.1:c.259-480A>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#.

36 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss11118904	Jul 11, 2003 (116)
2	SC_SNP	ss15451726	Feb 27, 2004 (120)
3	1000GENOMES	ss218624993	Jul 14, 2010 (132)
4	ILLUMINA	ss480925604	May 04, 2012 (137)
5	ILLUMINA	ss482087603	May 04, 2012 (137)
6	ILLUMINA	ss534027696	Sep 08, 2015 (146)
7	ILLUMINA	ss779808083	Aug 21, 2014 (142)
8	ILLUMINA	ss781352884	Aug 21, 2014 (142)
9	ILLUMINA	ss835284243	Aug 21, 2014 (142)
10	EVA-GONL	ss975626039	Aug 21, 2014 (142)
11	1000GENOMES	ss1292645483	Aug 21, 2014 (142)
12	EVA_DECODE	ss1585009074	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1601105917	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1644099950	Apr 01, 2015 (144)
15	WEILL_CORNELL_DGM	ss1918824465	Feb 12, 2016 (147)
16	HUMAN_LONGEVITY	ss2166154826	Dec 20, 2016 (150)
17	ILLUMINA	ss2632569921	Nov 08, 2017 (151)
18	GNOMAD	ss2760168538	Nov 08, 2017 (151)
19	ILLUMINA	ss3626195229	Oct 11, 2018 (152)
20	ILLUMINA	ss3630603234	Oct 11, 2018 (152)
21	ILLUMINA	ss3641614268	Oct 11, 2018 (152)
22	EVA_DECODE	ss3687634278	Jul 12, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3799738647	Jul 12, 2019 (153)
24	EVA	ss3826396980	Apr 25, 2020 (154)
25	SGDP_PRJ	ss3849757647	Apr 25, 2020 (154)
26	TOPMED	ss4465523990	Apr 25, 2021 (155)
27	TOPMED	ss4465523991	Apr 25, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5243791939	Oct 12, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5243791940	Oct 12, 2022 (156)
30	EVA	ss5321524939	Oct 12, 2022 (156)
31	HUGCELL_USP	ss5444696462	Oct 12, 2022 (156)
32	EVA	ss5506015027	Oct 12, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5516881743	Oct 12, 2022 (156)
34	SANFORD_IMAGENETICS	ss5626402134	Oct 12, 2022 (156)
35	EVA	ss5910013729	Oct 12, 2022 (156)
36	EVA	ss5938274726	Oct 12, 2022 (156)
37	1000Genomes	NC_000001.10 - 119577316	Oct 11, 2018 (152)
38	1000Genomes_30x	NC_000001.11 - 119034693	Oct 12, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 119577316	Oct 11, 2018 (152)
40	gnomAD - Genomes	NC_000001.11 - 119034693	Apr 25, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000001.10 - 119577316	Apr 25, 2020 (154)
42	Qatari	NC_000001.10 - 119577316	Apr 25, 2020 (154)
43	SGDP_PRJ	NC_000001.10 - 119577316	Apr 25, 2020 (154)
44	TopMed Submission ignored due to conflicting rows: Row 29130325 (NC_000001.11:119034692:T:C 5979/264690) Row 29130326 (NC_000001.11:119034692:T:G 3/264690)	-	Apr 25, 2021 (155)
45	TopMed Submission ignored due to conflicting rows: Row 29130325 (NC_000001.11:119034692:T:C 5979/264690) Row 29130326 (NC_000001.11:119034692:T:G 3/264690)	-	Apr 25, 2021 (155)
46	UK 10K study - Twins	NC_000001.10 - 119577316	Oct 11, 2018 (152)
47	ALFA	NC_000001.11 - 119034693	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss482087603, ss1585009074	NC_000001.9:119378838:T:C	NC_000001.11:119034692:T:C	(self)
3428593, 1900598, 826040, 866395, 1774627, 1900598, ss218624993, ss480925604, ss534027696, ss779808083, ss781352884, ss835284243, ss975626039, ss1292645483, ss1601105917, ss1644099950, ss1918824465, ss2632569921, ss2760168538, ss3626195229, ss3630603234, ss3641614268, ss3826396980, ss3849757647, ss5321524939, ss5506015027, ss5626402134, ss5938274726	NC_000001.10:119577315:T:C	NC_000001.11:119034692:T:C	(self)
4407678, 24250235, 7559756042, ss2166154826, ss3687634278, ss3799738647, ss4465523990, ss5243791939, ss5444696462, ss5516881743, ss5910013729	NC_000001.11:119034692:T:C	NC_000001.11:119034692:T:C	(self)
ss11118904	NT_004754.14:3492197:T:C	NC_000001.11:119034692:T:C	(self)
ss15451726	NT_032977.9:89549233:T:C	NC_000001.11:119034692:T:C	(self)
ss218624993	NC_000001.10:119577315:T:G	NC_000001.11:119034692:T:G	(self)
4407678, 7559756042, ss4465523991, ss5243791940, ss5516881743	NC_000001.11:119034692:T:G	NC_000001.11:119034692:T:G	(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 rs7354830

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

rs7354830