Name: rs2732707
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.

rs2732707

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:46274234 (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=0.109434 (14496/132464, GnomAD)
T=0.00046 (13/28258, 14KJPN)
T=0.00036 (6/16760, 8.3KJPN) (+ 13 more)
T=0.13758 (2247/16332, ALFA)
T=0.0782 (501/6404, 1000G_30x)
T=0.0787 (394/5008, 1000G)
T=0.0003 (1/2922, KOREAN)
T=0.212 (212/998, GoNL)
T=0.112 (67/600, NorthernSweden)
T=0.073 (39/534, MGP)
T=0.046 (14/304, HapMap)
T=0.162 (35/216, Qatari)
C=0.50 (40/80, SGDP_PRJ)
T=0.50 (40/80, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LRRC37A : Intron Variant
ARL17B : 3 Prime UTR Variant
LOC124904014 : 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	16332	C=0.86242	T=0.13758
European	Sub	12080	C=0.83733	T=0.16267
African	Sub	2816	C=0.9595	T=0.0405
African Others	Sub	108	C=0.991	T=0.009
African American	Sub	2708	C=0.9583	T=0.0417
Asian	Sub	108	C=1.000	T=0.000
East Asian	Sub	84	C=1.00	T=0.00
Other Asian	Sub	24	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.829	T=0.171
Latin American 2	Sub	610	C=0.880	T=0.120
South Asian	Sub	94	C=0.91	T=0.09
Other	Sub	478	C=0.870	T=0.130

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	132464	C=0.890566	T=0.109434
gnomAD - Genomes	European	Sub	70182	C=0.85150	T=0.14850
gnomAD - Genomes	African	Sub	41342	C=0.96367	T=0.03633
gnomAD - Genomes	American	Sub	12770	C=0.86273	T=0.13727
gnomAD - Genomes	East Asian	Sub	3130	C=0.9994	T=0.0006
gnomAD - Genomes	Ashkenazi Jewish	Sub	3046	C=0.8145	T=0.1855
gnomAD - Genomes	Other	Sub	1994	C=0.8736	T=0.1264
14KJPN	JAPANESE	Study-wide	28258	C=0.99954	T=0.00046
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99964	T=0.00036
Allele Frequency Aggregator	Total	Global	16332	C=0.86242	T=0.13758
Allele Frequency Aggregator	European	Sub	12080	C=0.83733	T=0.16267
Allele Frequency Aggregator	African	Sub	2816	C=0.9595	T=0.0405
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.880	T=0.120
Allele Frequency Aggregator	Other	Sub	478	C=0.870	T=0.130
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.829	T=0.171
Allele Frequency Aggregator	Asian	Sub	108	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	C=0.91	T=0.09
1000Genomes_30x	Global	Study-wide	6404	C=0.9218	T=0.0782
1000Genomes_30x	African	Sub	1786	C=0.9860	T=0.0140
1000Genomes_30x	Europe	Sub	1266	C=0.7891	T=0.2109
1000Genomes_30x	South Asian	Sub	1202	C=0.9393	T=0.0607
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=0.862	T=0.138
1000Genomes	Global	Study-wide	5008	C=0.9213	T=0.0787
1000Genomes	African	Sub	1322	C=0.9849	T=0.0151
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=0.7873	T=0.2127
1000Genomes	South Asian	Sub	978	C=0.941	T=0.059
1000Genomes	American	Sub	694	C=0.854	T=0.146
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9997	T=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.788	T=0.212
Northern Sweden	ACPOP	Study-wide	600	C=0.888	T=0.112
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.927	T=0.073
HapMap	Global	Study-wide	304	C=0.954	T=0.046
HapMap	African	Sub	112	C=1.000	T=0.000
HapMap	American	Sub	102	C=0.863	T=0.137
HapMap	Asian	Sub	90	C=1.00	T=0.00
Qatari	Global	Study-wide	216	C=0.838	T=0.162
SGDP_PRJ	Global	Study-wide	80	C=0.50	T=0.50
Siberian	Global	Study-wide	4	C=0.5	T=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 17	NC_000017.11:g.46274234C>T
GRCh37.p13 chr 17	NC_000017.10:g.44351600C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.512377A>G
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.514370A>G
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.976623C>T

Gene: ARL17B, ADP ribosylation factor like GTPase 17B (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARL17B transcript variant 2	NM_001103154.2:c.*1206=	N/A	3 Prime UTR Variant
ARL17B transcript variant 1	NM_001039083.5:c.	N/A	Genic Downstream Transcript Variant
ARL17B transcript variant 3	NM_001330240.1:c.	N/A	Genic Downstream Transcript Variant
ARL17B transcript variant 4	NM_001352769.1:c.	N/A	Genic Downstream Transcript Variant
ARL17B transcript variant 5	NM_001363805.1:c.	N/A	Genic Downstream Transcript Variant

Gene: LRRC37A, leucine rich repeat containing 37A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC37A transcript	NM_014834.4:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X9	XM_047437205.1:c.102-2556… XM_047437205.1:c.102-25560C>T	N/A	Intron Variant
LRRC37A transcript variant X1	XM_047437196.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X2	XM_047437197.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X3	XM_047437198.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X4	XM_047437199.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X10	XM_047437200.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X5	XM_047437201.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X6	XM_047437202.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X11	XM_047437203.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X7	XM_047437204.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X8	XM_047437206.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC124904014, uncharacterized LOC124904014 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124904014 transcript variant X1	XR_007065823.1:n.	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 17	NC_000017.11:g.46274234=	NC_000017.11:g.46274234C>T
GRCh37.p13 chr 17	NC_000017.10:g.44351600=	NC_000017.10:g.44351600C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.512377A>G	NT_167251.2:g.512377=
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.514370A>G	NT_167251.1:g.514370=
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.976623=	NT_187663.1:g.976623C>T
ARL17B transcript variant 2	NM_001103154.2:c.*1206=	NM_001103154.2:c.*1206G>A
LRRC37A transcript variant X9	XM_005257886.1:c.102-25560=	XM_005257886.1:c.102-25560C>T
LRRC37A transcript variant X10	XM_005257887.1:c.27-25560=	XM_005257887.1:c.27-25560C>T
LRRC37A transcript variant X9	XM_047437205.1:c.102-25560=	XM_047437205.1:c.102-25560C>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#.

34 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3857843	Sep 28, 2001 (100)
2	BCMHGSC_JDW	ss90600076	Mar 24, 2008 (129)
3	BUSHMAN	ss202551154	Jul 04, 2010 (132)
4	BCM-HGSC-SUB	ss207814665	Jul 04, 2010 (132)
5	1000GENOMES	ss237252650	Jul 15, 2010 (137)
6	SSMP	ss661092370	Apr 25, 2013 (138)
7	EVA-GONL	ss993133985	Aug 21, 2014 (142)
8	1000GENOMES	ss1358756895	Aug 21, 2014 (142)
9	EVA_MGP	ss1711463738	Apr 01, 2015 (144)
10	HAMMER_LAB	ss1808794690	Sep 08, 2015 (146)
11	WEILL_CORNELL_DGM	ss1936595379	Feb 12, 2016 (147)
12	JJLAB	ss2029074291	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2157547623	Dec 20, 2016 (150)
14	SWEGEN	ss3015580434	Nov 08, 2017 (151)
15	BIOINF_KMB_FNS_UNIBA	ss3028358685	Nov 08, 2017 (151)
16	EVA_DECODE	ss3700519775	Jul 13, 2019 (153)
17	ACPOP	ss3742048721	Jul 13, 2019 (153)
18	EVA	ss3754698201	Jul 13, 2019 (153)
19	PACBIO	ss3788214438	Jul 13, 2019 (153)
20	PACBIO	ss3793170217	Jul 13, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3819965851	Jul 13, 2019 (153)
22	EVA	ss3834881560	Apr 27, 2020 (154)
23	EVA	ss3841051831	Apr 27, 2020 (154)
24	EVA	ss3846548967	Apr 27, 2020 (154)
25	SGDP_PRJ	ss3885804069	Apr 27, 2020 (154)
26	KRGDB	ss3935504707	Apr 27, 2020 (154)
27	TOMMO_GENOMICS	ss5222545059	Apr 27, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5303227343	Oct 16, 2022 (156)
29	EVA	ss5427758821	Oct 16, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5606990634	Oct 16, 2022 (156)
31	SANFORD_IMAGENETICS	ss5660155083	Oct 16, 2022 (156)
32	TOMMO_GENOMICS	ss5778797650	Oct 16, 2022 (156)
33	EVA	ss5834020947	Oct 16, 2022 (156)
34	EVA	ss5951545803	Oct 16, 2022 (156)
35	1000Genomes	NC_000017.10 - 44351600	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000017.11 - 46274234	Oct 16, 2022 (156)
37	gnomAD - Genomes	NC_000017.11 - 46274234	Apr 27, 2021 (155)
38	Genome of the Netherlands Release 5	NC_000017.10 - 44351600	Apr 27, 2020 (154)
39	HapMap	NC_000017.11 - 46274234	Apr 27, 2020 (154)
40	KOREAN population from KRGDB	NC_000017.10 - 44351600	Apr 27, 2020 (154)
41	Medical Genome Project healthy controls from Spanish population	NC_000017.10 - 44351600	Apr 27, 2020 (154)
42	Northern Sweden	NC_000017.10 - 44351600	Jul 13, 2019 (153)
43	Qatari	NC_000017.10 - 44351600	Apr 27, 2020 (154)
44	SGDP_PRJ	NC_000017.10 - 44351600	Apr 27, 2020 (154)
45	Siberian	NC_000017.10 - 44351600	Apr 27, 2020 (154)
46	8.3KJPN	NC_000017.10 - 44351600	Apr 27, 2021 (155)
47	14KJPN	NC_000017.11 - 46274234	Oct 16, 2022 (156)
48	ALFA	NC_000017.11 - 46274234	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).

Associated ID	History Updated (Build)
rs117521858	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss90600076, ss202551154, ss207814665	NC_000017.9:41707376:C:T	NC_000017.11:46274233:C:T	(self)
72002617, 17784464, 42682101, 579498, 15333586, 18637301, 37821049, 10063977, 80514366, ss237252650, ss661092370, ss993133985, ss1358756895, ss1711463738, ss1808794690, ss1936595379, ss2029074291, ss2157547623, ss3015580434, ss3742048721, ss3754698201, ss3788214438, ss3793170217, ss3834881560, ss3841051831, ss3885804069, ss3935504707, ss5222545059, ss5427758821, ss5660155083, ss5834020947, ss5951545803	NC_000017.10:44351599:C:T	NC_000017.11:46274233:C:T	(self)
94516569, 508025740, 1492207, 112634754, 14356778538, ss3028358685, ss3700519775, ss3819965851, ss3846548967, ss5303227343, ss5606990634, ss5778797650	NC_000017.11:46274233:C:T	NC_000017.11:46274233:C:T	(self)
ss3857843	NT_010783.15:9625751:C:T	NC_000017.11:46274233: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 rs2732707

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
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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

rs2732707