Name: rs165948
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.

rs165948

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:168507388 (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=0.137312 (36345/264690, TOPMED)
T=0.142911 (20003/139968, GnomAD)
T=0.15495 (5208/33610, ALFA) (+ 18 more)
T=0.06423 (1815/28258, 14KJPN)
T=0.06444 (1080/16760, 8.3KJPN)
T=0.1145 (733/6404, 1000G_30x)
T=0.1158 (580/5008, 1000G)
T=0.1395 (625/4480, Estonian)
T=0.1842 (710/3854, ALSPAC)
T=0.1748 (648/3708, TWINSUK)
T=0.0763 (223/2922, KOREAN)
T=0.0759 (139/1832, Korea1K)
T=0.198 (198/998, GoNL)
T=0.183 (110/600, NorthernSweden)
T=0.278 (60/216, Qatari)
T=0.083 (18/216, Vietnamese)
T=0.058 (12/208, HapMap)
C=0.470 (62/132, SGDP_PRJ)
T=0.25 (10/40, GENOME_DK)
C=0.50 (9/18, Siberian)
T=0.50 (9/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RARS1 : 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	33610	C=0.84505	T=0.15495
European	Sub	24802	C=0.82578	T=0.17422
African	Sub	5780	C=0.9190	T=0.0810
African Others	Sub	206	C=0.961	T=0.039
African American	Sub	5574	C=0.9175	T=0.0825
Asian	Sub	130	C=0.892	T=0.108
East Asian	Sub	102	C=0.873	T=0.127
Other Asian	Sub	28	C=0.96	T=0.04
Latin American 1	Sub	168	C=0.827	T=0.173
Latin American 2	Sub	700	C=0.896	T=0.104
South Asian	Sub	116	C=0.810	T=0.190
Other	Sub	1914	C=0.8532	T=0.1468

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=0.862688	T=0.137312
gnomAD - Genomes	Global	Study-wide	139968	C=0.857089	T=0.142911
gnomAD - Genomes	European	Sub	75816	C=0.81638	T=0.18362
gnomAD - Genomes	African	Sub	41922	C=0.92524	T=0.07476
gnomAD - Genomes	American	Sub	13630	C=0.86354	T=0.13646
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.8285	T=0.1715
gnomAD - Genomes	East Asian	Sub	3130	C=0.9284	T=0.0716
gnomAD - Genomes	Other	Sub	2152	C=0.8629	T=0.1371
Allele Frequency Aggregator	Total	Global	33610	C=0.84505	T=0.15495
Allele Frequency Aggregator	European	Sub	24802	C=0.82578	T=0.17422
Allele Frequency Aggregator	African	Sub	5780	C=0.9190	T=0.0810
Allele Frequency Aggregator	Other	Sub	1914	C=0.8532	T=0.1468
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.896	T=0.104
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.827	T=0.173
Allele Frequency Aggregator	Asian	Sub	130	C=0.892	T=0.108
Allele Frequency Aggregator	South Asian	Sub	116	C=0.810	T=0.190
14KJPN	JAPANESE	Study-wide	28258	C=0.93577	T=0.06423
8.3KJPN	JAPANESE	Study-wide	16760	C=0.93556	T=0.06444
1000Genomes_30x	Global	Study-wide	6404	C=0.8855	T=0.1145
1000Genomes_30x	African	Sub	1786	C=0.9451	T=0.0549
1000Genomes_30x	Europe	Sub	1266	C=0.8144	T=0.1856
1000Genomes_30x	South Asian	Sub	1202	C=0.8419	T=0.1581
1000Genomes_30x	East Asian	Sub	1170	C=0.9179	T=0.0821
1000Genomes_30x	American	Sub	980	C=0.884	T=0.116
1000Genomes	Global	Study-wide	5008	C=0.8842	T=0.1158
1000Genomes	African	Sub	1322	C=0.9418	T=0.0582
1000Genomes	East Asian	Sub	1008	C=0.9127	T=0.0873
1000Genomes	Europe	Sub	1006	C=0.8211	T=0.1789
1000Genomes	South Asian	Sub	978	C=0.839	T=0.161
1000Genomes	American	Sub	694	C=0.888	T=0.112
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8605	T=0.1395
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8158	T=0.1842
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8252	T=0.1748
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9237	T=0.0763
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9241	T=0.0759
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.802	T=0.198
Northern Sweden	ACPOP	Study-wide	600	C=0.817	T=0.183
Qatari	Global	Study-wide	216	C=0.722	T=0.278
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.917	T=0.083
HapMap	Global	Study-wide	208	C=0.942	T=0.058
HapMap	African	Sub	118	C=0.966	T=0.034
HapMap	Asian	Sub	90	C=0.91	T=0.09
SGDP_PRJ	Global	Study-wide	132	C=0.470	T=0.530
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	18	C=0.50	T=0.50

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 5	NC_000005.10:g.168507388C>T
GRCh37.p13 chr 5	NC_000005.9:g.167934393C>T
RARS1 RefSeqGene	NG_041809.1:g.25931C>T

Gene: RARS1, arginyl-tRNA synthetase 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RARS1 transcript	NM_002887.4:c.1346+557C>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 5	NC_000005.10:g.168507388=	NC_000005.10:g.168507388C>T
GRCh37.p13 chr 5	NC_000005.9:g.167934393=	NC_000005.9:g.167934393C>T
RARS1 RefSeqGene	NG_041809.1:g.25931=	NG_041809.1:g.25931C>T
RARS transcript	NM_002887.3:c.1346+557=	NM_002887.3:c.1346+557C>T
RARS1 transcript	NM_002887.4:c.1346+557=	NM_002887.4:c.1346+557C>T
RARS transcript variant X1	XM_005265956.1:c.728+557=	XM_005265956.1:c.728+557C>T
RARS transcript variant X2	XM_005265957.1:c.728+557=	XM_005265957.1:c.728+557C>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#.

78 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss221373	Jul 12, 2000 (79)
2	SC_JCM	ss784351	Aug 11, 2000 (83)
3	KWOK	ss1196035	Oct 04, 2000 (86)
4	KWOK	ss2037518	Oct 18, 2000 (87)
5	TSC-CSHL	ss2227052	Oct 23, 2000 (88)
6	PERLEGEN	ss24671440	Sep 20, 2004 (123)
7	ABI	ss44586532	Mar 14, 2006 (126)
8	HUMANGENOME_JCVI	ss98786020	Feb 06, 2009 (130)
9	1000GENOMES	ss109610204	Jan 24, 2009 (130)
10	ENSEMBL	ss143375533	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss162872789	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss167350203	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss207046136	Jul 04, 2010 (132)
14	1000GENOMES	ss222105551	Jul 14, 2010 (132)
15	1000GENOMES	ss233248342	Jul 14, 2010 (132)
16	1000GENOMES	ss240350353	Jul 15, 2010 (132)
17	BL	ss253938405	May 09, 2011 (134)
18	GMI	ss278579109	May 04, 2012 (137)
19	PJP	ss293516985	May 09, 2011 (134)
20	ILLUMINA	ss483379459	May 04, 2012 (137)
21	ILLUMINA	ss484984996	May 04, 2012 (137)
22	ILLUMINA	ss535592385	Sep 08, 2015 (146)
23	TISHKOFF	ss558876134	Apr 25, 2013 (138)
24	SSMP	ss652785801	Apr 25, 2013 (138)
25	ILLUMINA	ss780255306	Sep 08, 2015 (146)
26	ILLUMINA	ss782132882	Sep 08, 2015 (146)
27	ILLUMINA	ss835741047	Sep 08, 2015 (146)
28	EVA-GONL	ss982390967	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1073242497	Aug 21, 2014 (142)
30	1000GENOMES	ss1318252156	Aug 21, 2014 (142)
31	DDI	ss1430577766	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1581454538	Apr 01, 2015 (144)
33	EVA_DECODE	ss1591932700	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1614569509	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1657563542	Apr 01, 2015 (144)
36	WEILL_CORNELL_DGM	ss1925641803	Feb 12, 2016 (147)
37	JJLAB	ss2023433459	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2151593753	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2280340869	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2626205134	Nov 08, 2017 (151)
41	ILLUMINA	ss2634373152	Nov 08, 2017 (151)
42	GRF	ss2707168935	Nov 08, 2017 (151)
43	GNOMAD	ss2833744770	Nov 08, 2017 (151)
44	SWEGEN	ss2998207876	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3025499641	Nov 08, 2017 (151)
46	CSHL	ss3346742927	Nov 08, 2017 (151)
47	ILLUMINA	ss3629399061	Oct 12, 2018 (152)
48	ILLUMINA	ss3632294785	Oct 12, 2018 (152)
49	ILLUMINA	ss3642460146	Oct 12, 2018 (152)
50	URBANLAB	ss3648223861	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3666142938	Jul 13, 2019 (153)
52	EVA_DECODE	ss3716210332	Jul 13, 2019 (153)
53	ACPOP	ss3733038114	Jul 13, 2019 (153)
54	EVA	ss3764383262	Jul 13, 2019 (153)
55	PACBIO	ss3785319312	Jul 13, 2019 (153)
56	PACBIO	ss3790691507	Jul 13, 2019 (153)
57	PACBIO	ss3795568628	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3807547203	Jul 13, 2019 (153)
59	EVA	ss3829632894	Apr 26, 2020 (154)
60	EVA	ss3838290117	Apr 26, 2020 (154)
61	EVA	ss3843733964	Apr 26, 2020 (154)
62	SGDP_PRJ	ss3863513353	Apr 26, 2020 (154)
63	KRGDB	ss3910219346	Apr 26, 2020 (154)
64	KOGIC	ss3958133205	Apr 26, 2020 (154)
65	TOPMED	ss4687780771	Apr 26, 2021 (155)
66	TOMMO_GENOMICS	ss5175316401	Apr 26, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5266750513	Oct 17, 2022 (156)
68	EVA	ss5315105170	Oct 17, 2022 (156)
69	EVA	ss5362643362	Oct 17, 2022 (156)
70	HUGCELL_USP	ss5464626518	Oct 17, 2022 (156)
71	EVA	ss5508300991	Oct 17, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5551874631	Oct 17, 2022 (156)
73	SANFORD_IMAGENETICS	ss5639394700	Oct 17, 2022 (156)
74	TOMMO_GENOMICS	ss5712731681	Oct 17, 2022 (156)
75	YY_MCH	ss5806986436	Oct 17, 2022 (156)
76	EVA	ss5835995896	Oct 17, 2022 (156)
77	EVA	ss5897376522	Oct 17, 2022 (156)
78	EVA	ss5967891473	Oct 17, 2022 (156)
79	1000Genomes	NC_000005.9 - 167934393	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000005.10 - 168507388	Oct 17, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 167934393	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000005.9 - 167934393	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000005.9 - 167934393	Apr 26, 2020 (154)
84	gnomAD - Genomes	NC_000005.10 - 168507388	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000005.9 - 167934393	Apr 26, 2020 (154)
86	HapMap	NC_000005.10 - 168507388	Apr 26, 2020 (154)
87	KOREAN population from KRGDB	NC_000005.9 - 167934393	Apr 26, 2020 (154)
88	Korean Genome Project	NC_000005.10 - 168507388	Apr 26, 2020 (154)
89	Northern Sweden	NC_000005.9 - 167934393	Jul 13, 2019 (153)
90	Qatari	NC_000005.9 - 167934393	Apr 26, 2020 (154)
91	SGDP_PRJ	NC_000005.9 - 167934393	Apr 26, 2020 (154)
92	Siberian	NC_000005.9 - 167934393	Apr 26, 2020 (154)
93	8.3KJPN	NC_000005.9 - 167934393	Apr 26, 2021 (155)
94	14KJPN	NC_000005.10 - 168507388	Oct 17, 2022 (156)
95	TopMed	NC_000005.10 - 168507388	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000005.9 - 167934393	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000005.9 - 167934393	Jul 13, 2019 (153)
98	ALFA	NC_000005.10 - 168507388	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).

Associated ID	History Updated (Build)
rs17552315	Oct 08, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss109610204, ss162872789, ss167350203, ss207046136, ss253938405, ss278579109, ss293516985, ss484984996, ss1591932700	NC_000005.8:167866970:C:T	NC_000005.10:168507387:C:T	(self)
29967620, 16681865, 11881186, 7619477, 7403658, 17396740, 6322979, 7683733, 15530333, 4110107, 33285708, 16681865, 3696638, ss222105551, ss233248342, ss240350353, ss483379459, ss535592385, ss558876134, ss652785801, ss780255306, ss782132882, ss835741047, ss982390967, ss1073242497, ss1318252156, ss1430577766, ss1581454538, ss1614569509, ss1657563542, ss1925641803, ss2023433459, ss2151593753, ss2626205134, ss2634373152, ss2707168935, ss2833744770, ss2998207876, ss3346742927, ss3629399061, ss3632294785, ss3642460146, ss3666142938, ss3733038114, ss3764383262, ss3785319312, ss3790691507, ss3795568628, ss3829632894, ss3838290117, ss3863513353, ss3910219346, ss5175316401, ss5315105170, ss5362643362, ss5508300991, ss5639394700, ss5835995896, ss5967891473	NC_000005.9:167934392:C:T	NC_000005.10:168507387:C:T	(self)
39400566, 211979196, 3022304, 14511206, 46568785, 525158328, 4192520677, ss2280340869, ss3025499641, ss3648223861, ss3716210332, ss3807547203, ss3843733964, ss3958133205, ss4687780771, ss5266750513, ss5464626518, ss5551874631, ss5712731681, ss5806986436, ss5897376522	NC_000005.10:168507387:C:T	NC_000005.10:168507387:C:T	(self)
ss221373, ss784351, ss1196035, ss2037518, ss2227052, ss24671440, ss44586532, ss98786020, ss143375533	NT_023133.13:12745665:C:T	NC_000005.10:168507387: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 rs165948

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

rs165948