Name: rs10513025
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.

rs10513025

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:9623510 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.056493 (14953/264690, TOPMED)
C=0.036241 (7542/208108, ALFA)
C=0.054785 (7682/140220, GnomAD) (+ 14 more)
C=0.06170 (4856/78700, PAGE_STUDY)
C=0.0542 (347/6404, 1000G_30x)
C=0.0517 (259/5008, 1000G)
C=0.0288 (129/4480, Estonian)
C=0.0330 (127/3854, ALSPAC)
C=0.0326 (121/3708, TWINSUK)
C=0.0685 (124/1810, HapMap)
C=0.034 (34/998, GoNL)
C=0.019 (12/626, Chileans)
C=0.015 (9/600, NorthernSweden)
C=0.106 (23/216, Qatari)
C=0.00 (0/86, Ancient Sardinia)
T=0.48 (26/54, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 12 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
Total	Global	208324	T=0.963754	C=0.036246
European	Sub	174596	T=0.964564	C=0.035436
African	Sub	7022	T=0.8943	C=0.1057
African Others	Sub	246	T=0.890	C=0.110
African American	Sub	6776	T=0.8945	C=0.1055
Asian	Sub	6666	T=0.9997	C=0.0003
East Asian	Sub	4776	T=0.9996	C=0.0004
Other Asian	Sub	1890	T=1.0000	C=0.0000
Latin American 1	Sub	936	T=0.946	C=0.054
Latin American 2	Sub	5386	T=0.9747	C=0.0253
South Asian	Sub	356	T=0.949	C=0.051
Other	Sub	13362	T=0.96894	C=0.03106

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	T=0.943507	C=0.056493
Allele Frequency Aggregator	Total	Global	208108	T=0.963759	C=0.036241
Allele Frequency Aggregator	European	Sub	174416	T=0.964556	C=0.035444
Allele Frequency Aggregator	Other	Sub	13340	T=0.96904	C=0.03096
Allele Frequency Aggregator	African	Sub	7008	T=0.8944	C=0.1056
Allele Frequency Aggregator	Asian	Sub	6666	T=0.9997	C=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	5386	T=0.9747	C=0.0253
Allele Frequency Aggregator	Latin American 1	Sub	936	T=0.946	C=0.054
Allele Frequency Aggregator	South Asian	Sub	356	T=0.949	C=0.051
gnomAD - Genomes	Global	Study-wide	140220	T=0.945215	C=0.054785
gnomAD - Genomes	European	Sub	75942	T=0.96692	C=0.03308
gnomAD - Genomes	African	Sub	42012	T=0.89332	C=0.10668
gnomAD - Genomes	American	Sub	13662	T=0.96904	C=0.03096
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9497	C=0.0503
gnomAD - Genomes	East Asian	Sub	3130	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2154	T=0.9550	C=0.0450
The PAGE Study	Global	Study-wide	78700	T=0.93830	C=0.06170
The PAGE Study	AfricanAmerican	Sub	32516	T=0.89550	C=0.10450
The PAGE Study	Mexican	Sub	10810	T=0.97438	C=0.02562
The PAGE Study	Asian	Sub	8318	T=0.9994	C=0.0006
The PAGE Study	PuertoRican	Sub	7918	T=0.9468	C=0.0532
The PAGE Study	NativeHawaiian	Sub	4534	T=0.9876	C=0.0124
The PAGE Study	Cuban	Sub	4230	T=0.9551	C=0.0449
The PAGE Study	Dominican	Sub	3828	T=0.9250	C=0.0750
The PAGE Study	CentralAmerican	Sub	2450	T=0.9645	C=0.0355
The PAGE Study	SouthAmerican	Sub	1982	T=0.9723	C=0.0277
The PAGE Study	NativeAmerican	Sub	1258	T=0.9610	C=0.0390
The PAGE Study	SouthAsian	Sub	856	T=0.964	C=0.036
1000Genomes_30x	Global	Study-wide	6404	T=0.9458	C=0.0542
1000Genomes_30x	African	Sub	1786	T=0.8802	C=0.1198
1000Genomes_30x	Europe	Sub	1266	T=0.9573	C=0.0427
1000Genomes_30x	South Asian	Sub	1202	T=0.9676	C=0.0324
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	T=0.960	C=0.040
1000Genomes	Global	Study-wide	5008	T=0.9483	C=0.0517
1000Genomes	African	Sub	1322	T=0.8805	C=0.1195
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.9543	C=0.0457
1000Genomes	South Asian	Sub	978	T=0.970	C=0.030
1000Genomes	American	Sub	694	T=0.964	C=0.036
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9712	C=0.0288
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9670	C=0.0330
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9674	C=0.0326
HapMap	Global	Study-wide	1810	T=0.9315	C=0.0685
HapMap	American	Sub	770	T=0.968	C=0.032
HapMap	African	Sub	692	T=0.877	C=0.123
HapMap	Europe	Sub	176	T=0.920	C=0.080
HapMap	Asian	Sub	172	T=1.000	C=0.000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.966	C=0.034
Chileans	Chilean	Study-wide	626	T=0.981	C=0.019
Northern Sweden	ACPOP	Study-wide	600	T=0.985	C=0.015
Qatari	Global	Study-wide	216	T=0.894	C=0.106
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	86	T=1.00	C=0.00
SGDP_PRJ	Global	Study-wide	54	T=0.48	C=0.52
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03

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.9623510T>C
GRCh37.p13 chr 5	NC_000005.9:g.9623622T>C

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
GRCh38.p14 chr 5	NC_000005.10:g.9623510=	NC_000005.10:g.9623510T>C
GRCh37.p13 chr 5	NC_000005.9:g.9623622=	NC_000005.9:g.9623622T>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#.

72 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss14911994	Dec 05, 2003 (119)
2	AFFY	ss66017600	Dec 02, 2006 (127)
3	AFFY	ss66506870	Dec 02, 2006 (127)
4	AFFY	ss76329837	Dec 07, 2007 (129)
5	KRIBB_YJKIM	ss82742325	Dec 15, 2007 (130)
6	ILLUMINA-UK	ss116470207	Feb 14, 2009 (130)
7	ILLUMINA	ss159907289	Dec 01, 2009 (131)
8	AFFY	ss173281468	Jul 04, 2010 (132)
9	BUSHMAN	ss199869541	Jul 04, 2010 (132)
10	1000GENOMES	ss221512080	Jul 14, 2010 (132)
11	1000GENOMES	ss232825403	Jul 14, 2010 (132)
12	ILLUMINA	ss479694971	Sep 08, 2015 (146)
13	EXOME_CHIP	ss491364427	May 04, 2012 (137)
14	TISHKOFF	ss558198144	Apr 25, 2013 (138)
15	ILLUMINA	ss780680579	Sep 08, 2015 (146)
16	ILLUMINA	ss783353859	Sep 08, 2015 (146)
17	EVA-GONL	ss981239704	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1072383382	Aug 21, 2014 (142)
19	1000GENOMES	ss1313870247	Aug 21, 2014 (142)
20	DDI	ss1430243353	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1581008670	Apr 01, 2015 (144)
22	EVA_DECODE	ss1590755507	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1612257246	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1655251279	Apr 01, 2015 (144)
25	EVA_SVP	ss1712743443	Apr 01, 2015 (144)
26	ILLUMINA	ss1752591006	Sep 08, 2015 (146)
27	HAMMER_LAB	ss1803047237	Sep 08, 2015 (146)
28	ILLUMINA	ss1917787981	Feb 12, 2016 (147)
29	WEILL_CORNELL_DGM	ss1924499856	Feb 12, 2016 (147)
30	ILLUMINA	ss1946138199	Feb 12, 2016 (147)
31	ILLUMINA	ss1958766122	Feb 12, 2016 (147)
32	JJLAB	ss2022847381	Sep 14, 2016 (149)
33	HUMAN_LONGEVITY	ss2271304279	Dec 20, 2016 (150)
34	ILLUMINA	ss2634244936	Nov 08, 2017 (151)
35	ILLUMINA	ss2634244937	Nov 08, 2017 (151)
36	GNOMAD	ss2821052666	Nov 08, 2017 (151)
37	AFFY	ss2985315478	Nov 08, 2017 (151)
38	SWEGEN	ss2996425172	Nov 08, 2017 (151)
39	ILLUMINA	ss3022465423	Nov 08, 2017 (151)
40	ILLUMINA	ss3629176184	Oct 12, 2018 (152)
41	ILLUMINA	ss3634990851	Oct 12, 2018 (152)
42	ILLUMINA	ss3636700235	Oct 12, 2018 (152)
43	ILLUMINA	ss3640698144	Oct 12, 2018 (152)
44	ILLUMINA	ss3644871082	Oct 12, 2018 (152)
45	ILLUMINA	ss3652958231	Oct 12, 2018 (152)
46	ILLUMINA	ss3654088224	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3664315629	Jul 13, 2019 (153)
48	EVA_DECODE	ss3714087837	Jul 13, 2019 (153)
49	ILLUMINA	ss3726212486	Jul 13, 2019 (153)
50	ACPOP	ss3732082259	Jul 13, 2019 (153)
51	ILLUMINA	ss3744533353	Jul 13, 2019 (153)
52	ILLUMINA	ss3745290985	Jul 13, 2019 (153)
53	EVA	ss3763056457	Jul 13, 2019 (153)
54	PAGE_CC	ss3771186149	Jul 13, 2019 (153)
55	ILLUMINA	ss3772785356	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3806223469	Jul 13, 2019 (153)
57	EVA	ss3829091179	Apr 26, 2020 (154)
58	SGDP_PRJ	ss3861194748	Apr 26, 2020 (154)
59	EVA	ss3985124757	Apr 26, 2021 (155)
60	TOPMED	ss4649305578	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5262847199	Oct 13, 2022 (156)
62	EVA	ss5355598574	Oct 13, 2022 (156)
63	HUGCELL_USP	ss5461196744	Oct 13, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5545881124	Oct 13, 2022 (156)
65	SANFORD_IMAGENETICS	ss5624582132	Oct 13, 2022 (156)
66	SANFORD_IMAGENETICS	ss5637167795	Oct 13, 2022 (156)
67	EVA	ss5834507870	Oct 13, 2022 (156)
68	EVA	ss5847261493	Oct 13, 2022 (156)
69	EVA	ss5848041151	Oct 13, 2022 (156)
70	EVA	ss5892957140	Oct 13, 2022 (156)
71	EVA	ss5965578573	Oct 13, 2022 (156)
72	EVA	ss5979731237	Oct 13, 2022 (156)
73	1000Genomes	NC_000005.9 - 9623622	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000005.10 - 9623510	Oct 13, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 9623622	Oct 12, 2018 (152)
76	Chileans	NC_000005.9 - 9623622	Apr 26, 2020 (154)
77	Genetic variation in the Estonian population	NC_000005.9 - 9623622	Oct 12, 2018 (152)
78	The Danish reference pan genome	NC_000005.9 - 9623622	Apr 26, 2020 (154)
79	gnomAD - Genomes	NC_000005.10 - 9623510	Apr 26, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000005.9 - 9623622	Apr 26, 2020 (154)
81	HapMap	NC_000005.10 - 9623510	Apr 26, 2020 (154)
82	Northern Sweden	NC_000005.9 - 9623622	Jul 13, 2019 (153)
83	The PAGE Study	NC_000005.10 - 9623510	Jul 13, 2019 (153)
84	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000005.9 - 9623622	Apr 26, 2021 (155)
85	Qatari	NC_000005.9 - 9623622	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000005.9 - 9623622	Apr 26, 2020 (154)
87	TopMed	NC_000005.10 - 9623510	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000005.9 - 9623622	Oct 12, 2018 (152)
89	ALFA	NC_000005.10 - 9623510	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)
rs60415715	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss116470207, ss199869541, ss1590755507, ss1712743443	NC_000005.8:9676621:T:C	NC_000005.10:9623509:T:C	(self)
25423780, 14146134, 339134, 10053877, 7173609, 6281174, 5367124, 350684, 6541786, 13211728, 14146134, ss221512080, ss232825403, ss479694971, ss491364427, ss558198144, ss780680579, ss783353859, ss981239704, ss1072383382, ss1313870247, ss1430243353, ss1581008670, ss1612257246, ss1655251279, ss1752591006, ss1803047237, ss1917787981, ss1924499856, ss1946138199, ss1958766122, ss2022847381, ss2634244936, ss2634244937, ss2821052666, ss2985315478, ss2996425172, ss3022465423, ss3629176184, ss3634990851, ss3636700235, ss3640698144, ss3644871082, ss3652958231, ss3654088224, ss3664315629, ss3732082259, ss3744533353, ss3745290985, ss3763056457, ss3772785356, ss3829091179, ss3861194748, ss3985124757, ss5355598574, ss5624582132, ss5637167795, ss5834507870, ss5847261493, ss5848041151, ss5965578573, ss5979731237	NC_000005.9:9623621:T:C	NC_000005.10:9623509:T:C	(self)
33407059, 179669848, 2807394, 407618, 486683135, 12884861708, ss2271304279, ss3714087837, ss3726212486, ss3771186149, ss3806223469, ss4649305578, ss5262847199, ss5461196744, ss5545881124, ss5892957140	NC_000005.10:9623509:T:C	NC_000005.10:9623509:T:C	(self)
ss14911994, ss66017600, ss66506870, ss76329837, ss82742325, ss159907289, ss173281468	NT_006576.16:9613621:T:C	NC_000005.10:9623509:T:C	(self)

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

12 citations for rs10513025

PMID	Title	Author	Year	Journal
19812673	A genome-wide linkage and association scan reveals novel loci for autism.	Weiss LA et al.	2009	Nature
21078308	Do common variants play a role in risk for autism? Evidence and theoretical musings.	Devlin B et al.	2011	Brain research
22739633	The association of rs4307059 and rs35678 markers with autism spectrum disorders is replicated in Italian families.	Prandini P et al.	2012	Psychiatric genetics
22843504	Individual common variants exert weak effects on the risk for autism spectrum disorders.	Anney R et al.	2012	Human molecular genetics
22849751	Autism genetics: searching for specificity and convergence.	Berg JM et al.	2012	Genome biology
23575222	An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk.	Cheng Y et al.	2013	Human molecular genetics
23620727	The evidence for association of ATP2B2 polymorphisms with autism in Chinese Han population.	Yang W et al.	2013	PloS one
23715297	Haplotype structure enables prioritization of common markers and candidate genes in autism spectrum disorder.	Vardarajan BN et al.	2013	Translational psychiatry
23840741	A Novel Stratification Method in Linkage Studies to Address Inter- and Intra-Family Heterogeneity in Autism.	Talebizadeh Z et al.	2013	PloS one
25360606	MACROD2 gene associated with autistic-like traits in a general population sample.	Jones RM et al.	2014	Psychiatric genetics
26395558	A de novo microdeletion of SEMA5A in a boy with autism spectrum disorder and intellectual disability.	Mosca-Boidron AL et al.	2016	European journal of human genetics
27417655	Lack of replication of previous autism spectrum disorder GWAS hits in European populations.	Torrico B et al.	2017	Autism research

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

rs10513025