Name: rs2671110
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.

rs2671110

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:132147298 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.285598 (75595/264690, TOPMED)
T=0.280697 (39347/140176, GnomAD)
T=0.06324 (1787/28258, 14KJPN) (+ 17 more)
T=0.18218 (3374/18520, ALFA)
T=0.06355 (1065/16758, 8.3KJPN)
T=0.3004 (1924/6404, 1000G_30x)
T=0.2853 (1429/5008, 1000G)
T=0.0717 (321/4480, Estonian)
T=0.0597 (230/3854, ALSPAC)
T=0.0620 (230/3708, TWINSUK)
T=0.0642 (188/2930, KOREAN)
T=0.060 (60/998, GoNL)
T=0.043 (26/600, NorthernSweden)
T=0.383 (121/316, HapMap)
T=0.208 (45/216, Qatari)
T=0.060 (13/216, Vietnamese)
G=0.273 (35/128, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
G=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PLXNA4 : Intron Variant
Publications: 1 citation
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	18520	G=0.81782	T=0.18218
European	Sub	14152	G=0.93428	T=0.06572
African	Sub	2898	G=0.2388	T=0.7612
African Others	Sub	114	G=0.079	T=0.921
African American	Sub	2784	G=0.2453	T=0.7547
Asian	Sub	112	G=0.938	T=0.062
East Asian	Sub	86	G=0.94	T=0.06
Other Asian	Sub	26	G=0.92	T=0.08
Latin American 1	Sub	146	G=0.781	T=0.219
Latin American 2	Sub	610	G=0.916	T=0.084
South Asian	Sub	98	G=0.91	T=0.09
Other	Sub	504	G=0.724	T=0.276

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=0.714402	T=0.285598
gnomAD - Genomes	Global	Study-wide	140176	G=0.719303	T=0.280697
gnomAD - Genomes	European	Sub	75928	G=0.92889	T=0.07111
gnomAD - Genomes	African	Sub	41984	G=0.25155	T=0.74845
gnomAD - Genomes	American	Sub	13654	G=0.88143	T=0.11857
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9185	T=0.0815
gnomAD - Genomes	East Asian	Sub	3134	G=0.9547	T=0.0453
gnomAD - Genomes	Other	Sub	2152	G=0.7709	T=0.2291
14KJPN	JAPANESE	Study-wide	28258	G=0.93676	T=0.06324
Allele Frequency Aggregator	Total	Global	18520	G=0.81782	T=0.18218
Allele Frequency Aggregator	European	Sub	14152	G=0.93428	T=0.06572
Allele Frequency Aggregator	African	Sub	2898	G=0.2388	T=0.7612
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.916	T=0.084
Allele Frequency Aggregator	Other	Sub	504	G=0.724	T=0.276
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.781	T=0.219
Allele Frequency Aggregator	Asian	Sub	112	G=0.938	T=0.062
Allele Frequency Aggregator	South Asian	Sub	98	G=0.91	T=0.09
8.3KJPN	JAPANESE	Study-wide	16758	G=0.93645	T=0.06355
1000Genomes_30x	Global	Study-wide	6404	G=0.6996	T=0.3004
1000Genomes_30x	African	Sub	1786	G=0.1204	T=0.8796
1000Genomes_30x	Europe	Sub	1266	G=0.9313	T=0.0687
1000Genomes_30x	South Asian	Sub	1202	G=0.9168	T=0.0832
1000Genomes_30x	East Asian	Sub	1170	G=0.9436	T=0.0564
1000Genomes_30x	American	Sub	980	G=0.898	T=0.102
1000Genomes	Global	Study-wide	5008	G=0.7147	T=0.2853
1000Genomes	African	Sub	1322	G=0.1271	T=0.8729
1000Genomes	East Asian	Sub	1008	G=0.9425	T=0.0575
1000Genomes	Europe	Sub	1006	G=0.9294	T=0.0706
1000Genomes	South Asian	Sub	978	G=0.920	T=0.080
1000Genomes	American	Sub	694	G=0.902	T=0.098
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9283	T=0.0717
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9403	T=0.0597
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9380	T=0.0620
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.9358	T=0.0642
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.940	T=0.060
Northern Sweden	ACPOP	Study-wide	600	G=0.957	T=0.043
HapMap	Global	Study-wide	316	G=0.617	T=0.383
HapMap	American	Sub	118	G=0.932	T=0.068
HapMap	African	Sub	116	G=0.034	T=0.966
HapMap	Asian	Sub	82	G=0.99	T=0.01
Qatari	Global	Study-wide	216	G=0.792	T=0.208
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.940	T=0.060
SGDP_PRJ	Global	Study-wide	128	G=0.273	T=0.727
The Danish reference pan genome	Danish	Study-wide	40	G=0.95	T=0.05
Siberian	Global	Study-wide	2	G=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 7	NC_000007.14:g.132147298G>T
GRCh37.p13 chr 7	NC_000007.13:g.131832057G>T

Gene: PLXNA4, plexin A4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLXNA4 transcript variant 4	NM_001393897.1:c.4865-598… NM_001393897.1:c.4865-598C>A	N/A	Intron Variant
PLXNA4 transcript variant 1	NM_020911.2:c.4865-598C>A	N/A	Intron Variant
PLXNA4 transcript variant 3	NM_001105543.2:c.	N/A	Genic Downstream Transcript Variant
PLXNA4 transcript variant 2	NM_181775.4:c.	N/A	Genic Downstream Transcript Variant
PLXNA4 transcript variant X1	XM_006716171.5:c.4865-598… XM_006716171.5:c.4865-598C>A	N/A	Intron Variant
PLXNA4 transcript variant X3	XM_017012779.1:c.4664-598… XM_017012779.1:c.4664-598C>A	N/A	Intron Variant
PLXNA4 transcript variant X2	XM_047421017.1:c.4865-598… XM_047421017.1:c.4865-598C>A	N/A	Intron Variant
PLXNA4 transcript variant X4	XM_011516676.3:c.	N/A	Genic Downstream Transcript Variant
PLXNA4 transcript variant X7	XM_047421018.1:c.	N/A	Genic Downstream Transcript Variant
PLXNA4 transcript variant X6	XM_047421019.1:c.	N/A	Genic Downstream Transcript Variant
PLXNA4 transcript variant X5	XR_927546.3:n.	N/A	Genic Downstream 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	G=	T
GRCh38.p14 chr 7	NC_000007.14:g.132147298=	NC_000007.14:g.132147298G>T
GRCh37.p13 chr 7	NC_000007.13:g.131832057=	NC_000007.13:g.131832057G>T
PLXNA4 transcript variant 4	NM_001393897.1:c.4865-598=	NM_001393897.1:c.4865-598C>A
PLXNA4 transcript variant 1	NM_020911.1:c.4865-598=	NM_020911.1:c.4865-598C>A
PLXNA4 transcript variant 1	NM_020911.2:c.4865-598=	NM_020911.2:c.4865-598C>A
PLXNA4 transcript variant X1	XM_005250686.1:c.4865-598=	XM_005250686.1:c.4865-598C>A
PLXNA4 transcript variant X1	XM_006716171.5:c.4865-598=	XM_006716171.5:c.4865-598C>A
PLXNA4 transcript variant X3	XM_017012779.1:c.4664-598=	XM_017012779.1:c.4664-598C>A
PLXNA4 transcript variant X2	XM_047421017.1:c.4865-598=	XM_047421017.1:c.4865-598C>A

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#.

55 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3769194	Sep 28, 2001 (100)
2	BCM_SSAHASNP	ss10388940	Jul 11, 2003 (116)
3	WUGSC_SSAHASNP	ss14564474	Dec 05, 2003 (120)
4	HGSV	ss85499660	Dec 16, 2007 (130)
5	1000GENOMES	ss114449997	Jan 25, 2009 (130)
6	ILLUMINA-UK	ss116315488	Feb 14, 2009 (130)
7	COMPLETE_GENOMICS	ss165428390	Jul 04, 2010 (132)
8	BUSHMAN	ss198293178	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss208255405	Jul 04, 2010 (132)
10	1000GENOMES	ss223339426	Jul 14, 2010 (132)
11	1000GENOMES	ss234174030	Jul 15, 2010 (132)
12	GMI	ss285721838	Apr 25, 2013 (138)
13	TISHKOFF	ss560314287	Apr 25, 2013 (138)
14	SSMP	ss654724952	Apr 25, 2013 (138)
15	EVA-GONL	ss984818506	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1074995929	Aug 21, 2014 (142)
17	1000GENOMES	ss1327215476	Aug 21, 2014 (142)
18	DDI	ss1431284947	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1582409637	Apr 01, 2015 (144)
20	EVA_DECODE	ss1594407214	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1619256915	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1662250948	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1805227147	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1928075852	Feb 12, 2016 (147)
25	JJLAB	ss2024726861	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2152948578	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2298024594	Dec 20, 2016 (150)
28	GRF	ss2708667675	Nov 08, 2017 (151)
29	GNOMAD	ss2859341796	Nov 08, 2017 (151)
30	SWEGEN	ss3002067418	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3026152719	Nov 08, 2017 (151)
32	CSHL	ss3347853007	Nov 08, 2017 (151)
33	EGCUT_WGS	ss3669823248	Jul 13, 2019 (153)
34	ACPOP	ss3735089393	Jul 13, 2019 (153)
35	EVA	ss3767184315	Jul 13, 2019 (153)
36	PACBIO	ss3785964026	Jul 13, 2019 (153)
37	PACBIO	ss3791241898	Jul 13, 2019 (153)
38	PACBIO	ss3796122064	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3810353648	Jul 13, 2019 (153)
40	EVA	ss3830830437	Apr 26, 2020 (154)
41	SGDP_PRJ	ss3868438517	Apr 26, 2020 (154)
42	KRGDB	ss3915793951	Apr 26, 2020 (154)
43	TOPMED	ss4764477285	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5185677916	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5274811008	Oct 13, 2022 (156)
46	EVA	ss5376910491	Oct 13, 2022 (156)
47	HUGCELL_USP	ss5471689747	Oct 13, 2022 (156)
48	EVA	ss5509143863	Oct 13, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5564004440	Oct 13, 2022 (156)
50	SANFORD_IMAGENETICS	ss5644027900	Oct 13, 2022 (156)
51	TOMMO_GENOMICS	ss5726700989	Oct 13, 2022 (156)
52	YY_MCH	ss5809110375	Oct 13, 2022 (156)
53	EVA	ss5823553711	Oct 13, 2022 (156)
54	EVA	ss5860966546	Oct 13, 2022 (156)
55	EVA	ss5973226778	Oct 13, 2022 (156)
56	1000Genomes	NC_000007.13 - 131832057	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000007.14 - 132147298	Oct 13, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 131832057	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000007.13 - 131832057	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000007.13 - 131832057	Apr 26, 2020 (154)
61	gnomAD - Genomes	NC_000007.14 - 132147298	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000007.13 - 131832057	Apr 26, 2020 (154)
63	HapMap	NC_000007.14 - 132147298	Apr 26, 2020 (154)
64	KOREAN population from KRGDB	NC_000007.13 - 131832057	Apr 26, 2020 (154)
65	Northern Sweden	NC_000007.13 - 131832057	Jul 13, 2019 (153)
66	Qatari	NC_000007.13 - 131832057	Apr 26, 2020 (154)
67	SGDP_PRJ	NC_000007.13 - 131832057	Apr 26, 2020 (154)
68	Siberian	NC_000007.13 - 131832057	Apr 26, 2020 (154)
69	8.3KJPN	NC_000007.13 - 131832057	Apr 26, 2021 (155)
70	14KJPN	NC_000007.14 - 132147298	Oct 13, 2022 (156)
71	TopMed	NC_000007.14 - 132147298	Apr 26, 2021 (155)
72	UK 10K study - Twins	NC_000007.13 - 131832057	Oct 12, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000007.13 - 131832057	Jul 13, 2019 (153)
74	ALFA	NC_000007.14 - 132147298	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)
rs10359101	Feb 27, 2004 (120)
rs61576978	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85499660	NC_000007.11:131289311:G:T	NC_000007.14:132147297:G:T	(self)
ss114449997, ss116315488, ss165428390, ss198293178, ss208255405, ss285721838, ss1594407214	NC_000007.12:131482596:G:T	NC_000007.14:132147297:G:T	(self)
39262510, 21846545, 15561496, 8574575, 9748405, 22971345, 8374258, 10117782, 20455497, 5464932, 43647223, 21846545, 4866210, ss223339426, ss234174030, ss560314287, ss654724952, ss984818506, ss1074995929, ss1327215476, ss1431284947, ss1582409637, ss1619256915, ss1662250948, ss1805227147, ss1928075852, ss2024726861, ss2152948578, ss2708667675, ss2859341796, ss3002067418, ss3347853007, ss3669823248, ss3735089393, ss3767184315, ss3785964026, ss3791241898, ss3796122064, ss3830830437, ss3868438517, ss3915793951, ss5185677916, ss5376910491, ss5509143863, ss5644027900, ss5823553711, ss5973226778	NC_000007.13:131832056:G:T	NC_000007.14:132147297:G:T	(self)
51530375, 277260864, 3497037, 60538093, 601854844, 9828376692, ss2298024594, ss3026152719, ss3810353648, ss4764477285, ss5274811008, ss5471689747, ss5564004440, ss5726700989, ss5809110375, ss5860966546	NC_000007.14:132147297:G:T	NC_000007.14:132147297:G:T	(self)
ss10388940	NT_007933.12:56870483:G:T	NC_000007.14:132147297:G:T	(self)
ss14564474	NT_007933.13:56870483:G:T	NC_000007.14:132147297:G:T	(self)
ss3769194	NT_007933.15:69864899:G:T	NC_000007.14:132147297:G:T	(self)

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

1 citation for rs2671110

PMID	Title	Author	Year	Journal
21296741	Ancestry-informative markers on chromosomes 2, 8 and 15 are associated with insulin-related traits in a racially diverse sample of children.	Klimentidis YC et al.	2011	Human genomics

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

rs2671110