Name: rs34882979
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.

rs34882979

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:58862829-58862838 (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: delTT / delT / dupT
Variation Type: Indel Insertion and Deletion
Frequency: (T)₁₀=0.113941 (30159/264690, TOPMED)
(T)₁₀=0.1491 (737/4944, 1000G)
(T)₁₀=0.0607 (281/4632, ALFA) (+ 7 more)
(T)₁₀=0.0261 (117/4480, Estonian)
(T)₁₀=0.0221 (85/3854, ALSPAC)
(T)₁₀=0.0202 (75/3708, TWINSUK)
(T)₁₀=0.1616 (296/1832, Korea1K)
(T)₁₀=0.014 (14/998, GoNL)
(T)₁₀=0.028 (17/600, NorthernSweden)
(T)₁₀=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GLYATL2 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	4632	TTTTTTTTTT=0.0607	TTTTTTTT=0.0000, TTTTTTTTT=0.9393, TTTTTTTTTTT=0.0000	0.035406	0.914076	0.050518	32
European	Sub	4466	TTTTTTTTTT=0.0275	TTTTTTTT=0.0000, TTTTTTTTT=0.9725, TTTTTTTTTTT=0.0000	0.001343	0.946261	0.052396	1
African	Sub	142	TTTTTTTTTT=1.000	TTTTTTTT=0.000, TTTTTTTTT=0.000, TTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
African Others	Sub	8	TTTTTTTTTT=1.0	TTTTTTTT=0.0, TTTTTTTTT=0.0, TTTTTTTTTTT=0.0	1.0	0.0	0.0	N/A
African American	Sub	134	TTTTTTTTTT=1.000	TTTTTTTT=0.000, TTTTTTTTT=0.000, TTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
Asian	Sub	0	TTTTTTTTTT=0	TTTTTTTT=0, TTTTTTTTT=0, TTTTTTTTTTT=0	0	0	0	N/A
East Asian	Sub	0	TTTTTTTTTT=0	TTTTTTTT=0, TTTTTTTTT=0, TTTTTTTTTTT=0	0	0	0	N/A
Other Asian	Sub	0	TTTTTTTTTT=0	TTTTTTTT=0, TTTTTTTTT=0, TTTTTTTTTTT=0	0	0	0	N/A
Latin American 1	Sub	0	TTTTTTTTTT=0	TTTTTTTT=0, TTTTTTTTT=0, TTTTTTTTTTT=0	0	0	0	N/A
Latin American 2	Sub	6	TTTTTTTTTT=1.0	TTTTTTTT=0.0, TTTTTTTTT=0.0, TTTTTTTTTTT=0.0	1.0	0.0	0.0	N/A
South Asian	Sub	0	TTTTTTTTTT=0	TTTTTTTT=0, TTTTTTTTT=0, TTTTTTTTTTT=0	0	0	0	N/A
Other	Sub	18	TTTTTTTTTT=0.56	TTTTTTTT=0.00, TTTTTTTTT=0.44, TTTTTTTTTTT=0.00	0.555556	0.444444	0.0	5

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	(T)₁₀=0.113941	delT=0.886059
1000Genomes	Global	Study-wide	4944	(T)₁₀=0.1491	delT=0.8509
1000Genomes	African	Sub	1262	(T)₁₀=0.3146	delT=0.6854
1000Genomes	East Asian	Sub	1008	(T)₁₀=0.1419	delT=0.8581
1000Genomes	Europe	Sub	1006	(T)₁₀=0.0249	delT=0.9751
1000Genomes	South Asian	Sub	977	(T)₁₀=0.124	delT=0.876
1000Genomes	American	Sub	691	(T)₁₀=0.074	delT=0.926
Allele Frequency Aggregator	Total	Global	4632	(T)₁₀=0.0607	delTT=0.0000, delT=0.9393, dupT=0.0000
Allele Frequency Aggregator	European	Sub	4466	(T)₁₀=0.0275	delTT=0.0000, delT=0.9725, dupT=0.0000
Allele Frequency Aggregator	African	Sub	142	(T)₁₀=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Other	Sub	18	(T)₁₀=0.56	delTT=0.00, delT=0.44, dupT=0.00
Allele Frequency Aggregator	Latin American 2	Sub	6	(T)₁₀=1.0	delTT=0.0, delT=0.0, dupT=0.0
Allele Frequency Aggregator	Latin American 1	Sub	0	(T)₁₀=0	delTT=0, delT=0, dupT=0
Allele Frequency Aggregator	South Asian	Sub	0	(T)₁₀=0	delTT=0, delT=0, dupT=0
Allele Frequency Aggregator	Asian	Sub	0	(T)₁₀=0	delTT=0, delT=0, dupT=0
Genetic variation in the Estonian population	Estonian	Study-wide	4480	(T)₁₀=0.0261	delT=0.9739
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(T)₁₀=0.0221	delT=0.9779
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(T)₁₀=0.0202	delT=0.9798
Korean Genome Project	KOREAN	Study-wide	1832	(T)₁₀=0.1616	delT=0.8384
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	(T)₁₀=0.014	delT=0.986
Northern Sweden	ACPOP	Study-wide	600	(T)₁₀=0.028	delT=0.972
The Danish reference pan genome	Danish	Study-wide	40	(T)₁₀=0.03	delT=0.97

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 11	NC_000011.10:g.58862837_58862838del
GRCh38.p14 chr 11	NC_000011.10:g.58862838del
GRCh38.p14 chr 11	NC_000011.10:g.58862838dup
GRCh37.p13 chr 11	NC_000011.9:g.58630310_58630311del
GRCh37.p13 chr 11	NC_000011.9:g.58630311del
GRCh37.p13 chr 11	NC_000011.9:g.58630311dup

Gene: GLYATL2, glycine-N-acyltransferase like 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GLYATL2 transcript	NM_145016.4:c.	N/A	Genic Upstream Transcript Variant
GLYATL2 transcript variant X2	XM_017017338.3:c.-40-2317… XM_017017338.3:c.-40-23178_-40-23177del	N/A	Intron Variant
GLYATL2 transcript variant X1	XM_017017337.3:c.	N/A	Genic Upstream Transcript Variant
GLYATL2 transcript variant X3	XM_047426545.1:c.	N/A	Genic Upstream Transcript 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)₁₀=	delTT	delT	dupT
GRCh38.p14 chr 11	NC_000011.10:g.58862829_58862838=	NC_000011.10:g.58862837_58862838del	NC_000011.10:g.58862838del	NC_000011.10:g.58862838dup
GRCh37.p13 chr 11	NC_000011.9:g.58630302_58630311=	NC_000011.9:g.58630310_58630311del	NC_000011.9:g.58630311del	NC_000011.9:g.58630311dup
GLYATL2 transcript variant X2	XM_017017338.3:c.-40-23177=	XM_017017338.3:c.-40-23178_-40-23177del	XM_017017338.3:c.-40-23177del	XM_017017338.3:c.-40-23177dup

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#.

62 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss39951771	Mar 14, 2006 (126)
2	HGSV	ss80239637	Sep 08, 2015 (146)
3	HUMANGENOME_JCVI	ss95569704	Feb 06, 2009 (137)
4	GMI	ss155407044	Dec 01, 2009 (131)
5	BUSHMAN	ss193232869	Jul 04, 2010 (132)
6	GMI	ss287876143	May 09, 2011 (134)
7	GMI	ss289071973	May 04, 2012 (137)
8	PJP	ss294705118	May 09, 2011 (134)
9	1000GENOMES	ss327342753	May 09, 2011 (137)
10	1000GENOMES	ss327430195	May 09, 2011 (137)
11	1000GENOMES	ss327839532	May 09, 2011 (137)
12	LUNTER	ss552131532	Apr 25, 2013 (138)
13	LUNTER	ss552389597	Apr 25, 2013 (138)
14	LUNTER	ss553450778	Apr 25, 2013 (138)
15	TISHKOFF	ss554585304	Apr 25, 2013 (138)
16	SSMP	ss664060070	Apr 01, 2015 (144)
17	BILGI_BIOE	ss666536877	Apr 25, 2013 (138)
18	EVA-GONL	ss988566619	Aug 21, 2014 (142)
19	1000GENOMES	ss1370957573	Aug 21, 2014 (142)
20	1000GENOMES	ss1370957576	Aug 21, 2014 (142)
21	DDI	ss1536692143	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1574359173	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1707117750	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1707117778	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1806834958	Sep 08, 2015 (146)
26	JJLAB	ss2031079101	Sep 14, 2016 (149)
27	SYSTEMSBIOZJU	ss2627828036	Nov 08, 2017 (151)
28	SWEGEN	ss3008164136	Nov 08, 2017 (151)
29	MCHAISSO	ss3063693594	Nov 08, 2017 (151)
30	MCHAISSO	ss3064518424	Nov 08, 2017 (151)
31	MCHAISSO	ss3065431325	Nov 08, 2017 (151)
32	BEROUKHIMLAB	ss3644321237	Oct 12, 2018 (152)
33	BIOINF_KMB_FNS_UNIBA	ss3645199156	Oct 12, 2018 (152)
34	URBANLAB	ss3649621368	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3675503216	Jul 13, 2019 (153)
36	EVA_DECODE	ss3691868369	Jul 13, 2019 (153)
37	ACPOP	ss3738217307	Jul 13, 2019 (153)
38	PACBIO	ss3786965670	Jul 13, 2019 (153)
39	PACBIO	ss3792105794	Jul 13, 2019 (153)
40	PACBIO	ss3796988138	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3814693920	Jul 13, 2019 (153)
42	EVA	ss3832650997	Apr 26, 2020 (154)
43	EVA	ss3839883678	Apr 26, 2020 (154)
44	EVA	ss3845362919	Apr 26, 2020 (154)
45	KOGIC	ss3969974929	Apr 26, 2020 (154)
46	GNOMAD	ss4235802302	Apr 26, 2021 (155)
47	GNOMAD	ss4235802303	Apr 26, 2021 (155)
48	GNOMAD	ss4235802304	Apr 26, 2021 (155)
49	TOPMED	ss4886709412	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5202165849	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5202165850	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5287564142	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5287564143	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5287564144	Oct 16, 2022 (156)
55	HUGCELL_USP	ss5482729183	Oct 16, 2022 (156)
56	HUGCELL_USP	ss5482729184	Oct 16, 2022 (156)
57	TOMMO_GENOMICS	ss5750097245	Oct 16, 2022 (156)
58	TOMMO_GENOMICS	ss5750097246	Oct 16, 2022 (156)
59	YY_MCH	ss5812451494	Oct 16, 2022 (156)
60	EVA	ss5836718330	Oct 16, 2022 (156)
61	EVA	ss5920142759	Oct 16, 2022 (156)
62	EVA	ss5942621646	Oct 16, 2022 (156)
63	1000Genomes	NC_000011.9 - 58630302	Oct 12, 2018 (152)
64	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 58630302	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000011.9 - 58630302	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000011.9 - 58630302	Apr 26, 2020 (154)
67	gnomAD - Genomes Submission ignored due to conflicting rows: Row 380942319 (NC_000011.10:58862828::T 2143/139530) Row 380942320 (NC_000011.10:58862828:T: 123391/139504) Row 380942321 (NC_000011.10:58862828:TT: 4/139540)	-	Apr 26, 2021 (155)
68	gnomAD - Genomes Submission ignored due to conflicting rows: Row 380942319 (NC_000011.10:58862828::T 2143/139530) Row 380942320 (NC_000011.10:58862828:T: 123391/139504) Row 380942321 (NC_000011.10:58862828:TT: 4/139540)	-	Apr 26, 2021 (155)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 380942319 (NC_000011.10:58862828::T 2143/139530) Row 380942320 (NC_000011.10:58862828:T: 123391/139504) Row 380942321 (NC_000011.10:58862828:TT: 4/139540)	-	Apr 26, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000011.9 - 58630302	Apr 26, 2020 (154)
71	Korean Genome Project	NC_000011.10 - 58862829	Apr 26, 2020 (154)
72	Northern Sweden	NC_000011.9 - 58630302	Jul 13, 2019 (153)
73	8.3KJPN Submission ignored due to conflicting rows: Row 60135156 (NC_000011.9:58630301:T: 14869/16758) Row 60135157 (NC_000011.9:58630301::T 4/16758)	-	Apr 26, 2021 (155)
74	8.3KJPN Submission ignored due to conflicting rows: Row 60135156 (NC_000011.9:58630301:T: 14869/16758) Row 60135157 (NC_000011.9:58630301::T 4/16758)	-	Apr 26, 2021 (155)
75	14KJPN Submission ignored due to conflicting rows: Row 83934349 (NC_000011.10:58862828:T: 25059/28258) Row 83934350 (NC_000011.10:58862828::T 8/28258)	-	Oct 16, 2022 (156)
76	14KJPN Submission ignored due to conflicting rows: Row 83934349 (NC_000011.10:58862828:T: 25059/28258) Row 83934350 (NC_000011.10:58862828::T 8/28258)	-	Oct 16, 2022 (156)
77	TopMed	NC_000011.10 - 58862829	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000011.9 - 58630302	Oct 12, 2018 (152)
79	ALFA	NC_000011.10 - 58862829	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)
rs60367293	May 11, 2012 (137)
rs149533203	May 04, 2012 (137)
rs375460993	May 13, 2013 (138)
rs377514135	May 15, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4235802304, ss5287564144	NC_000011.10:58862828:TT:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTT	(self)
11195355580	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTT	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTT	(self)
ss289071973, ss294705118, ss327342753, ss327430195, ss327839532, ss552131532, ss552389597, ss553450778	NC_000011.8:58386877:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss80239637	NC_000011.8:58386886:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
53970416, 29971113, 21241464, 298957, 13376289, 11502172, 29971113, ss664060070, ss666536877, ss988566619, ss1370957573, ss1536692143, ss1574359173, ss1707117750, ss1707117778, ss1806834958, ss2031079101, ss2627828036, ss3008164136, ss3644321237, ss3675503216, ss3738217307, ss3786965670, ss3792105794, ss3796988138, ss3832650997, ss3839883678, ss5202165849, ss5836718330, ss5942621646	NC_000011.9:58630301:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss554585304	NC_000011.9:58630310:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
26352930, 102255068, ss3063693594, ss3064518424, ss3065431325, ss3645199156, ss3649621368, ss3691868369, ss3814693920, ss3845362919, ss3969974929, ss4235802303, ss4886709412, ss5287564142, ss5482729183, ss5750097245, ss5812451494, ss5920142759	NC_000011.10:58862828:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
11195355580	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss39951771, ss155407044, ss287876143	NT_167190.1:3936096:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss95569704	NT_167190.1:3936105:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss193232869	NT_167190.2:4337754:T:	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTT	(self)
ss5202165850	NC_000011.9:58630301::T	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTTTT	(self)
ss1370957576	NC_000011.9:58630302::T	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTTTT	(self)
ss4235802302, ss5287564143, ss5482729184, ss5750097246	NC_000011.10:58862828::T	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTTTT	(self)
11195355580	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTTTT	NC_000011.10:58862828:TTTTTTTTTT:T… NC_000011.10:58862828:TTTTTTTTTT:TTTTTTTTTTT	(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 rs34882979

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs34882979