Name: rs10987876
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.

rs10987876

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:128107808 (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=0.152480 (40360/264690, TOPMED)
T=0.149755 (21001/140236, GnomAD)
T=0.15373 (4744/30860, ALFA) (+ 15 more)
T=0.19669 (5558/28258, 14KJPN)
T=0.19946 (3343/16760, 8.3KJPN)
T=0.1757 (1125/6404, 1000G_30x)
T=0.1795 (899/5008, 1000G)
T=0.1654 (741/4480, Estonian)
T=0.1583 (610/3854, ALSPAC)
T=0.1629 (604/3708, TWINSUK)
T=0.1799 (527/2930, KOREAN)
T=0.179 (179/998, GoNL)
T=0.107 (64/600, NorthernSweden)
T=0.185 (40/216, Qatari)
T=0.093 (20/214, Vietnamese)
C=0.421 (85/202, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC25A25 : Non Coding Transcript 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	30860	C=0.84627	T=0.15373
European	Sub	24730	C=0.84311	T=0.15689
African	Sub	3168	C=0.8857	T=0.1143
African Others	Sub	124	C=0.847	T=0.153
African American	Sub	3044	C=0.8873	T=0.1127
Asian	Sub	128	C=0.867	T=0.133
East Asian	Sub	100	C=0.86	T=0.14
Other Asian	Sub	28	C=0.89	T=0.11
Latin American 1	Sub	168	C=0.863	T=0.137
Latin American 2	Sub	700	C=0.796	T=0.204
South Asian	Sub	114	C=0.711	T=0.289
Other	Sub	1852	C=0.8456	T=0.1544

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=0.847520	T=0.152480
gnomAD - Genomes	Global	Study-wide	140236	C=0.850245	T=0.149755
gnomAD - Genomes	European	Sub	75942	C=0.83923	T=0.16077
gnomAD - Genomes	African	Sub	42028	C=0.88379	T=0.11621
gnomAD - Genomes	American	Sub	13658	C=0.80385	T=0.19615
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.8538	T=0.1462
gnomAD - Genomes	East Asian	Sub	3130	C=0.8783	T=0.1217
gnomAD - Genomes	Other	Sub	2154	C=0.8319	T=0.1681
Allele Frequency Aggregator	Total	Global	30860	C=0.84627	T=0.15373
Allele Frequency Aggregator	European	Sub	24730	C=0.84311	T=0.15689
Allele Frequency Aggregator	African	Sub	3168	C=0.8857	T=0.1143
Allele Frequency Aggregator	Other	Sub	1852	C=0.8456	T=0.1544
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.796	T=0.204
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.863	T=0.137
Allele Frequency Aggregator	Asian	Sub	128	C=0.867	T=0.133
Allele Frequency Aggregator	South Asian	Sub	114	C=0.711	T=0.289
14KJPN	JAPANESE	Study-wide	28258	C=0.80331	T=0.19669
8.3KJPN	JAPANESE	Study-wide	16760	C=0.80054	T=0.19946
1000Genomes_30x	Global	Study-wide	6404	C=0.8243	T=0.1757
1000Genomes_30x	African	Sub	1786	C=0.8695	T=0.1305
1000Genomes_30x	Europe	Sub	1266	C=0.8436	T=0.1564
1000Genomes_30x	South Asian	Sub	1202	C=0.7196	T=0.2804
1000Genomes_30x	East Asian	Sub	1170	C=0.8675	T=0.1325
1000Genomes_30x	American	Sub	980	C=0.794	T=0.206
1000Genomes	Global	Study-wide	5008	C=0.8205	T=0.1795
1000Genomes	African	Sub	1322	C=0.8707	T=0.1293
1000Genomes	East Asian	Sub	1008	C=0.8601	T=0.1399
1000Genomes	Europe	Sub	1006	C=0.8479	T=0.1521
1000Genomes	South Asian	Sub	978	C=0.703	T=0.297
1000Genomes	American	Sub	694	C=0.793	T=0.207
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8346	T=0.1654
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8417	T=0.1583
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8371	T=0.1629
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8201	T=0.1799
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.821	T=0.179
Northern Sweden	ACPOP	Study-wide	600	C=0.893	T=0.107
Qatari	Global	Study-wide	216	C=0.815	T=0.185
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.907	T=0.093
SGDP_PRJ	Global	Study-wide	202	C=0.421	T=0.579
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	T=0.12
Siberian	Global	Study-wide	20	C=0.45	T=0.55

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 9	NC_000009.12:g.128107808C>T
GRCh37.p13 chr 9	NC_000009.11:g.130870087C>T
SLC25A25 RefSeqGene	NG_032871.1:g.44609C>T

Gene: SLC25A25, solute carrier family 25 member 25 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC25A25 transcript variant 5	NM_001265614.3:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 2	NM_001006641.4:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 3	NM_001006642.4:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 6	NM_001330988.2:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 1	NM_052901.5:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 7	NM_001387057.1:c.*364=	N/A	3 Prime UTR Variant
SLC25A25 transcript variant 4	NR_049766.3:n.1877C>T	N/A	Non Coding 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	C=	T
GRCh38.p14 chr 9	NC_000009.12:g.128107808=	NC_000009.12:g.128107808C>T
GRCh37.p13 chr 9	NC_000009.11:g.130870087=	NC_000009.11:g.130870087C>T
SLC25A25 RefSeqGene	NG_032871.1:g.44609=	NG_032871.1:g.44609C>T
SLC25A25 transcript variant 1	NM_052901.5:c.*364=	NM_052901.5:c.*364C>T
SLC25A25 transcript variant 1	NM_052901.4:c.*364=	NM_052901.4:c.*364C>T
SLC25A25 transcript variant 3	NM_001006642.4:c.*364=	NM_001006642.4:c.*364C>T
SLC25A25 transcript variant 3	NM_001006642.3:c.*364=	NM_001006642.3:c.*364C>T
SLC25A25 transcript variant 2	NM_001006641.4:c.*364=	NM_001006641.4:c.*364C>T
SLC25A25 transcript variant 2	NM_001006641.3:c.*364=	NM_001006641.3:c.*364C>T
SLC25A25 transcript variant 5	NM_001265614.3:c.*364=	NM_001265614.3:c.*364C>T
SLC25A25 transcript variant 5	NM_001265614.2:c.*364=	NM_001265614.2:c.*364C>T
SLC25A25 transcript variant 4	NR_049766.3:n.1877=	NR_049766.3:n.1877C>T
SLC25A25 transcript variant 4	NR_049766.2:n.1902=	NR_049766.2:n.1902C>T
SLC25A25 transcript variant 6	NM_001330988.2:c.*364=	NM_001330988.2:c.*364C>T
SLC25A25 transcript variant 6	NM_001330988.1:c.*364=	NM_001330988.1:c.*364C>T
SLC25A25 transcript variant 7	NM_001387057.1:c.*364=	NM_001387057.1:c.*364C>T
SLC25A25 transcript variant 4	NM_001006643.1:c.*364=	NM_001006643.1:c.*364C>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#.

74 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16176752	Feb 27, 2004 (120)
2	SC_SNP	ss18594150	Feb 27, 2004 (120)
3	SI_EXO	ss52068450	Oct 15, 2006 (127)
4	1000GENOMES	ss109090323	Jan 23, 2009 (130)
5	GMI	ss157997309	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss164915937	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss166970293	Jul 04, 2010 (132)
8	ILLUMINA	ss168926167	Jul 04, 2010 (132)
9	BUSHMAN	ss200916441	Jul 04, 2010 (132)
10	1000GENOMES	ss224469123	Jul 14, 2010 (132)
11	1000GENOMES	ss234981442	Jul 15, 2010 (132)
12	1000GENOMES	ss241728033	Jul 15, 2010 (132)
13	GMI	ss280411359	May 04, 2012 (137)
14	ILLUMINA	ss480979372	May 04, 2012 (137)
15	ILLUMINA	ss485733520	May 04, 2012 (137)
16	ILLUMINA	ss534060422	Sep 08, 2015 (146)
17	TISHKOFF	ss561654680	Apr 25, 2013 (138)
18	SSMP	ss656150120	Apr 25, 2013 (138)
19	ILLUMINA	ss779814434	Sep 08, 2015 (146)
20	ILLUMINA	ss781366383	Sep 08, 2015 (146)
21	ILLUMINA	ss835290703	Sep 08, 2015 (146)
22	EVA-GONL	ss987012474	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1076632289	Aug 21, 2014 (142)
24	1000GENOMES	ss1335580935	Aug 21, 2014 (142)
25	DDI	ss1431969427	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1583270302	Apr 01, 2015 (144)
27	EVA_DECODE	ss1596656927	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1623634003	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1666628036	Apr 01, 2015 (144)
30	HAMMER_LAB	ss1806173614	Sep 08, 2015 (146)
31	WEILL_CORNELL_DGM	ss1930324644	Feb 12, 2016 (147)
32	GENOMED	ss1971314862	Jul 19, 2016 (147)
33	JJLAB	ss2025885653	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2154117250	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2314702628	Dec 20, 2016 (150)
36	ILLUMINA	ss2634921018	Nov 08, 2017 (151)
37	GRF	ss2710000970	Nov 08, 2017 (151)
38	GNOMAD	ss2883569462	Nov 08, 2017 (151)
39	SWEGEN	ss3005640710	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3026724582	Nov 08, 2017 (151)
41	CSHL	ss3348869636	Nov 08, 2017 (151)
42	ILLUMINA	ss3630363640	Oct 12, 2018 (152)
43	ILLUMINA	ss3632810229	Oct 12, 2018 (152)
44	ILLUMINA	ss3638838042	Oct 12, 2018 (152)
45	ILLUMINA	ss3642714095	Oct 12, 2018 (152)
46	URBANLAB	ss3649244420	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3673184999	Jul 13, 2019 (153)
48	EVA_DECODE	ss3724812809	Jul 13, 2019 (153)
49	ACPOP	ss3736901919	Jul 13, 2019 (153)
50	EVA	ss3769729602	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3812891724	Jul 13, 2019 (153)
52	EVA	ss3825763575	Apr 26, 2020 (154)
53	EVA	ss3831875003	Apr 26, 2020 (154)
54	EVA	ss3839466547	Apr 26, 2020 (154)
55	EVA	ss3844931500	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3873133869	Apr 26, 2020 (154)
57	KRGDB	ss3921021043	Apr 26, 2020 (154)
58	FSA-LAB	ss3984430091	Apr 26, 2021 (155)
59	TOPMED	ss4836779496	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5195440947	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5282286161	Oct 16, 2022 (156)
62	EVA	ss5315435625	Oct 16, 2022 (156)
63	EVA	ss5390459530	Oct 16, 2022 (156)
64	HUGCELL_USP	ss5478144950	Oct 16, 2022 (156)
65	EVA	ss5509859427	Oct 16, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5575400685	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5648324721	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5740014393	Oct 16, 2022 (156)
69	YY_MCH	ss5811030851	Oct 16, 2022 (156)
70	EVA	ss5829790418	Oct 16, 2022 (156)
71	EVA	ss5856948241	Oct 16, 2022 (156)
72	EVA	ss5918153536	Oct 16, 2022 (156)
73	EVA	ss5977539061	Oct 16, 2022 (156)
74	EVA	ss5980579655	Oct 16, 2022 (156)
75	1000Genomes	NC_000009.11 - 130870087	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000009.12 - 128107808	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 130870087	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000009.11 - 130870087	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000009.11 - 130870087	Apr 26, 2020 (154)
80	gnomAD - Genomes	NC_000009.12 - 128107808	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000009.11 - 130870087	Apr 26, 2020 (154)
82	KOREAN population from KRGDB	NC_000009.11 - 130870087	Apr 26, 2020 (154)
83	Northern Sweden	NC_000009.11 - 130870087	Jul 13, 2019 (153)
84	Qatari	NC_000009.11 - 130870087	Apr 26, 2020 (154)
85	SGDP_PRJ	NC_000009.11 - 130870087	Apr 26, 2020 (154)
86	Siberian	NC_000009.11 - 130870087	Apr 26, 2020 (154)
87	8.3KJPN	NC_000009.11 - 130870087	Apr 26, 2021 (155)
88	14KJPN	NC_000009.12 - 128107808	Oct 16, 2022 (156)
89	TopMed	NC_000009.12 - 128107808	Apr 26, 2021 (155)
90	UK 10K study - Twins	NC_000009.11 - 130870087	Oct 12, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000009.11 - 130870087	Jul 13, 2019 (153)
92	ALFA	NC_000009.12 - 128107808	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss109090323, ss164915937, ss166970293, ss200916441, ss280411359, ss485733520, ss1596656927	NC_000009.10:129909907:C:T	NC_000009.12:128107807:C:T	(self)
47903389, 26626519, 18923247, 9435239, 11877080, 28198437, 10186784, 12366574, 25150849, 6633604, 53410254, 26626519, 5911961, ss224469123, ss234981442, ss241728033, ss480979372, ss534060422, ss561654680, ss656150120, ss779814434, ss781366383, ss835290703, ss987012474, ss1076632289, ss1335580935, ss1431969427, ss1583270302, ss1623634003, ss1666628036, ss1806173614, ss1930324644, ss1971314862, ss2025885653, ss2154117250, ss2634921018, ss2710000970, ss2883569462, ss3005640710, ss3348869636, ss3630363640, ss3632810229, ss3638838042, ss3642714095, ss3673184999, ss3736901919, ss3769729602, ss3825763575, ss3831875003, ss3839466547, ss3873133869, ss3921021043, ss3984430091, ss5195440947, ss5315435625, ss5390459530, ss5509859427, ss5648324721, ss5829790418, ss5977539061, ss5980579655	NC_000009.11:130870086:C:T	NC_000009.12:128107807:C:T	(self)
62926620, 338567704, 73851497, 674157057, 3032949633, ss2314702628, ss3026724582, ss3649244420, ss3724812809, ss3812891724, ss3844931500, ss4836779496, ss5282286161, ss5478144950, ss5575400685, ss5740014393, ss5811030851, ss5856948241, ss5918153536	NC_000009.12:128107807:C:T	NC_000009.12:128107807:C:T	(self)
ss16176752, ss18594150	NT_008470.16:32527821:C:T	NC_000009.12:128107807:C:T	(self)
ss52068450	NT_008470.17:38191290:C:T	NC_000009.12:128107807:C:T	(self)
ss157997309, ss168926167	NT_008470.19:60034618:C:T	NC_000009.12:128107807: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 rs10987876

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

rs10987876