Name: rs12118018
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.

rs12118018

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154504964 (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>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.488164 (129212/264690, TOPMED)
A=0.494131 (69118/139878, GnomAD)
G=0.26451 (7474/28256, 14KJPN) (+ 16 more)
G=0.45590 (8612/18890, ALFA)
G=0.26301 (4408/16760, 8.3KJPN)
A=0.4986 (3193/6404, 1000G_30x)
G=0.4896 (2452/5008, 1000G)
G=0.4368 (1957/4480, Estonian)
G=0.3544 (1366/3854, ALSPAC)
G=0.3514 (1303/3708, TWINSUK)
G=0.1836 (538/2930, KOREAN)
G=0.1725 (316/1832, Korea1K)
G=0.358 (357/998, GoNL)
G=0.418 (251/600, NorthernSweden)
G=0.250 (109/436, SGDP_PRJ)
G=0.491 (106/216, Qatari)
G=0.335 (71/212, Vietnamese)
G=0.34 (17/50, Siberian)
G=0.40 (16/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TDRD10 : 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	18890	G=0.45590	A=0.54410
European	Sub	14286	G=0.38989	A=0.61011
African	Sub	2946	G=0.8109	A=0.1891
African Others	Sub	114	G=0.912	A=0.088
African American	Sub	2832	G=0.8069	A=0.1931
Asian	Sub	112	G=0.241	A=0.759
East Asian	Sub	86	G=0.24	A=0.76
Other Asian	Sub	26	G=0.23	A=0.77
Latin American 1	Sub	146	G=0.418	A=0.582
Latin American 2	Sub	610	G=0.279	A=0.721
South Asian	Sub	98	G=0.46	A=0.54
Other	Sub	692	G=0.506	A=0.494

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=0.488164	A=0.511836
gnomAD - Genomes	Global	Study-wide	139878	G=0.505869	A=0.494131
gnomAD - Genomes	European	Sub	75804	G=0.39239	A=0.60761
gnomAD - Genomes	African	Sub	41866	G=0.80385	A=0.19615
gnomAD - Genomes	American	Sub	13606	G=0.32353	A=0.67647
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.3721	A=0.6279
gnomAD - Genomes	East Asian	Sub	3126	G=0.2310	A=0.7690
gnomAD - Genomes	Other	Sub	2152	G=0.4647	A=0.5353
14KJPN	JAPANESE	Study-wide	28256	G=0.26451	A=0.73549
Allele Frequency Aggregator	Total	Global	18890	G=0.45590	A=0.54410
Allele Frequency Aggregator	European	Sub	14286	G=0.38989	A=0.61011
Allele Frequency Aggregator	African	Sub	2946	G=0.8109	A=0.1891
Allele Frequency Aggregator	Other	Sub	692	G=0.506	A=0.494
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.279	A=0.721
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.418	A=0.582
Allele Frequency Aggregator	Asian	Sub	112	G=0.241	A=0.759
Allele Frequency Aggregator	South Asian	Sub	98	G=0.46	A=0.54
8.3KJPN	JAPANESE	Study-wide	16760	G=0.26301	A=0.73699
1000Genomes_30x	Global	Study-wide	6404	G=0.5014	A=0.4986
1000Genomes_30x	African	Sub	1786	G=0.8852	A=0.1148
1000Genomes_30x	Europe	Sub	1266	G=0.4115	A=0.5885
1000Genomes_30x	South Asian	Sub	1202	G=0.4226	A=0.5774
1000Genomes_30x	East Asian	Sub	1170	G=0.2590	A=0.7410
1000Genomes_30x	American	Sub	980	G=0.304	A=0.696
1000Genomes	Global	Study-wide	5008	G=0.4896	A=0.5104
1000Genomes	African	Sub	1322	G=0.8820	A=0.1180
1000Genomes	East Asian	Sub	1008	G=0.2599	A=0.7401
1000Genomes	Europe	Sub	1006	G=0.4066	A=0.5934
1000Genomes	South Asian	Sub	978	G=0.422	A=0.578
1000Genomes	American	Sub	694	G=0.291	A=0.709
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.4368	A=0.5632
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.3544	A=0.6456
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.3514	A=0.6486
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.1836	A=0.8164, C=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.1725	A=0.8275
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.358	A=0.642
Northern Sweden	ACPOP	Study-wide	600	G=0.418	A=0.582
SGDP_PRJ	Global	Study-wide	436	G=0.250	A=0.750
Qatari	Global	Study-wide	216	G=0.491	A=0.509
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.335	A=0.665
Siberian	Global	Study-wide	50	G=0.34	A=0.66
The Danish reference pan genome	Danish	Study-wide	40	G=0.40	A=0.60

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 1	NC_000001.11:g.154504964G>A
GRCh38.p14 chr 1	NC_000001.11:g.154504964G>C
GRCh37.p13 chr 1	NC_000001.10:g.154477440G>A
GRCh37.p13 chr 1	NC_000001.10:g.154477440G>C

Gene: TDRD10, tudor domain containing 10 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TDRD10 transcript variant 1	NM_001098475.2:c.-27-1913… NM_001098475.2:c.-27-1913G>A	N/A	Intron Variant
TDRD10 transcript variant 2	NM_182499.4:c.-27-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X1	XM_011509152.3:c.-48-1913… XM_011509152.3:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X2	XM_011509153.3:c.-48-1913… XM_011509153.3:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X3	XM_011509154.3:c.-27-1913… XM_011509154.3:c.-27-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X4	XM_011509155.3:c.-48-1913… XM_011509155.3:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X5	XM_011509156.3:c.-48-1913… XM_011509156.3:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X6	XM_011509157.3:c.-48-1913… XM_011509157.3:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X15	XM_047444646.1:c.-48-1913… XM_047444646.1:c.-48-1913G>A	N/A	Intron Variant
TDRD10 transcript variant X7	XM_011509158.2:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X8	XM_011509159.4:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X10	XM_011509160.2:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X11	XM_011509161.1:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X9	XM_017000255.1:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X12	XM_047444641.1:c.	N/A	Genic Upstream Transcript Variant
TDRD10 transcript variant X13	XR_007076384.1:n.	N/A	Intron Variant
TDRD10 transcript variant X14	XR_007076385.1: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	G=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.154504964=	NC_000001.11:g.154504964G>A	NC_000001.11:g.154504964G>C
GRCh37.p13 chr 1	NC_000001.10:g.154477440=	NC_000001.10:g.154477440G>A	NC_000001.10:g.154477440G>C
TDRD10 transcript variant 1	NM_001098475.1:c.-27-1913=	NM_001098475.1:c.-27-1913G>A	NM_001098475.1:c.-27-1913G>C
TDRD10 transcript variant 1	NM_001098475.2:c.-27-1913=	NM_001098475.2:c.-27-1913G>A	NM_001098475.2:c.-27-1913G>C
TDRD10 transcript variant 2	NM_182499.3:c.-27-1913=	NM_182499.3:c.-27-1913G>A	NM_182499.3:c.-27-1913G>C
TDRD10 transcript variant 2	NM_182499.4:c.-27-1913=	NM_182499.4:c.-27-1913G>A	NM_182499.4:c.-27-1913G>C
TDRD10 transcript variant X1	XM_005244886.1:c.-341-1913=	XM_005244886.1:c.-341-1913G>A	XM_005244886.1:c.-341-1913G>C
TDRD10 transcript variant X2	XM_005244887.1:c.-27-1913=	XM_005244887.1:c.-27-1913G>A	XM_005244887.1:c.-27-1913G>C
TDRD10 transcript variant X3	XM_005244888.1:c.-341-1913=	XM_005244888.1:c.-341-1913G>A	XM_005244888.1:c.-341-1913G>C
TDRD10 transcript variant X4	XM_005244889.1:c.-341-1913=	XM_005244889.1:c.-341-1913G>A	XM_005244889.1:c.-341-1913G>C
TDRD10 transcript variant X5	XM_005244890.1:c.-341-1913=	XM_005244890.1:c.-341-1913G>A	XM_005244890.1:c.-341-1913G>C
TDRD10 transcript variant X1	XM_011509152.3:c.-48-1913=	XM_011509152.3:c.-48-1913G>A	XM_011509152.3:c.-48-1913G>C
TDRD10 transcript variant X2	XM_011509153.3:c.-48-1913=	XM_011509153.3:c.-48-1913G>A	XM_011509153.3:c.-48-1913G>C
TDRD10 transcript variant X3	XM_011509154.3:c.-27-1913=	XM_011509154.3:c.-27-1913G>A	XM_011509154.3:c.-27-1913G>C
TDRD10 transcript variant X4	XM_011509155.3:c.-48-1913=	XM_011509155.3:c.-48-1913G>A	XM_011509155.3:c.-48-1913G>C
TDRD10 transcript variant X5	XM_011509156.3:c.-48-1913=	XM_011509156.3:c.-48-1913G>A	XM_011509156.3:c.-48-1913G>C
TDRD10 transcript variant X6	XM_011509157.3:c.-48-1913=	XM_011509157.3:c.-48-1913G>A	XM_011509157.3:c.-48-1913G>C
TDRD10 transcript variant X15	XM_047444646.1:c.-48-1913=	XM_047444646.1:c.-48-1913G>A	XM_047444646.1:c.-48-1913G>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#.

67 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18245980	Feb 28, 2004 (120)
2	SSAHASNP	ss20467881	Apr 05, 2004 (121)
3	ABI	ss41206143	Mar 15, 2006 (126)
4	HGSV	ss77758020	Dec 07, 2007 (129)
5	HGSV	ss78700626	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss87824451	Mar 23, 2008 (129)
7	HUMANGENOME_JCVI	ss97974811	Feb 06, 2009 (130)
8	BGI	ss106602089	Feb 06, 2009 (130)
9	ENSEMBL	ss138083209	Dec 01, 2009 (131)
10	ENSEMBL	ss143985741	Dec 01, 2009 (131)
11	GMI	ss155751990	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss167132912	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss205455356	Jul 04, 2010 (132)
14	1000GENOMES	ss230731748	Jul 14, 2010 (132)
15	BL	ss253508636	May 09, 2011 (134)
16	GMI	ss276051007	May 04, 2012 (137)
17	GMI	ss284152502	Apr 25, 2013 (138)
18	PJP	ss290636952	May 09, 2011 (134)
19	TISHKOFF	ss554693319	Apr 25, 2013 (138)
20	SSMP	ss648413694	Apr 25, 2013 (138)
21	EVA-GONL	ss975682082	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1068269265	Aug 21, 2014 (142)
23	1000GENOMES	ss1292923604	Aug 21, 2014 (142)
24	DDI	ss1425978778	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1574391689	Apr 01, 2015 (144)
26	EVA_DECODE	ss1585063457	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1601212886	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1644206919	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1918916025	Feb 12, 2016 (147)
30	GENOMED	ss1966867414	Jul 19, 2016 (147)
31	JJLAB	ss2019973505	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2147997991	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2166537015	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2624494715	Nov 08, 2017 (151)
35	GRF	ss2697970864	Nov 08, 2017 (151)
36	GNOMAD	ss2761310125	Nov 08, 2017 (151)
37	SWEGEN	ss2987751289	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3023743877	Nov 08, 2017 (151)
39	CSHL	ss3343710293	Nov 08, 2017 (151)
40	URBANLAB	ss3646791193	Oct 11, 2018 (152)
41	EGCUT_WGS	ss3655691368	Jul 12, 2019 (153)
42	EVA_DECODE	ss3687781300	Jul 12, 2019 (153)
43	ACPOP	ss3727485284	Jul 12, 2019 (153)
44	EVA	ss3746807441	Jul 12, 2019 (153)
45	PACBIO	ss3783566123	Jul 12, 2019 (153)
46	PACBIO	ss3789197694	Jul 12, 2019 (153)
47	PACBIO	ss3794069700	Jul 12, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3799809276	Jul 12, 2019 (153)
49	EVA	ss3826423846	Apr 25, 2020 (154)
50	EVA	ss3836606432	Apr 25, 2020 (154)
51	EVA	ss3842015652	Apr 25, 2020 (154)
52	SGDP_PRJ	ss3850005722	Apr 25, 2020 (154)
53	KRGDB	ss3895211732	Apr 25, 2020 (154)
54	KOGIC	ss3945649992	Apr 25, 2020 (154)
55	TOPMED	ss4468283822	Apr 25, 2021 (155)
56	TOMMO_GENOMICS	ss5146480555	Apr 25, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5244291358	Oct 17, 2022 (156)
58	HUGCELL_USP	ss5444884964	Oct 17, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5517618571	Oct 17, 2022 (156)
60	SANFORD_IMAGENETICS	ss5626590565	Oct 17, 2022 (156)
61	TOMMO_GENOMICS	ss5673675498	Oct 17, 2022 (156)
62	YY_MCH	ss5801259697	Oct 17, 2022 (156)
63	EVA	ss5832664880	Oct 17, 2022 (156)
64	EVA	ss5849108695	Oct 17, 2022 (156)
65	EVA	ss5910243616	Oct 17, 2022 (156)
66	EVA	ss5938384370	Oct 17, 2022 (156)
67	EVA	ss5979989980	Oct 17, 2022 (156)
68	1000Genomes	NC_000001.10 - 154477440	Oct 11, 2018 (152)
69	1000Genomes_30x	NC_000001.11 - 154504964	Oct 17, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154477440	Oct 11, 2018 (152)
71	Genetic variation in the Estonian population	NC_000001.10 - 154477440	Oct 11, 2018 (152)
72	The Danish reference pan genome	NC_000001.10 - 154477440	Apr 25, 2020 (154)
73	gnomAD - Genomes	NC_000001.11 - 154504964	Apr 25, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000001.10 - 154477440	Apr 25, 2020 (154)
75	KOREAN population from KRGDB	NC_000001.10 - 154477440	Apr 25, 2020 (154)
76	Korean Genome Project	NC_000001.11 - 154504964	Apr 25, 2020 (154)
77	Northern Sweden	NC_000001.10 - 154477440	Jul 12, 2019 (153)
78	Qatari	NC_000001.10 - 154477440	Apr 25, 2020 (154)
79	SGDP_PRJ	NC_000001.10 - 154477440	Apr 25, 2020 (154)
80	Siberian	NC_000001.10 - 154477440	Apr 25, 2020 (154)
81	8.3KJPN	NC_000001.10 - 154477440	Apr 25, 2021 (155)
82	14KJPN	NC_000001.11 - 154504964	Oct 17, 2022 (156)
83	TopMed	NC_000001.11 - 154504964	Apr 25, 2021 (155)
84	UK 10K study - Twins	NC_000001.10 - 154477440	Oct 11, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000001.10 - 154477440	Jul 12, 2019 (153)
86	ALFA	NC_000001.11 - 154504964	Apr 25, 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
ss77758020, ss78700626	NC_000001.8:151290512:G:A	NC_000001.11:154504963:G:A	(self)
ss87824451, ss167132912, ss205455356, ss253508636, ss276051007, ss284152502, ss290636952, ss1585063457	NC_000001.9:152744063:G:A	NC_000001.11:154504963:G:A	(self)
3715570, 2019974, 1429616, 1708448, 877752, 2389126, 770149, 957955, 2022702, 514345, 4449862, 2019974, 434138, ss230731748, ss554693319, ss648413694, ss975682082, ss1068269265, ss1292923604, ss1425978778, ss1574391689, ss1601212886, ss1644206919, ss1918916025, ss1966867414, ss2019973505, ss2147997991, ss2624494715, ss2697970864, ss2761310125, ss2987751289, ss3343710293, ss3655691368, ss3727485284, ss3746807441, ss3783566123, ss3789197694, ss3794069700, ss3826423846, ss3836606432, ss3850005722, ss3895211732, ss5146480555, ss5626590565, ss5832664880, ss5938384370, ss5979989980	NC_000001.10:154477439:G:A	NC_000001.11:154504963:G:A	(self)
5144506, 27036070, 2027993, 7512602, 31890157, 6398602509, ss2166537015, ss3023743877, ss3646791193, ss3687781300, ss3799809276, ss3842015652, ss3945649992, ss4468283822, ss5244291358, ss5444884964, ss5517618571, ss5673675498, ss5801259697, ss5849108695, ss5910243616	NC_000001.11:154504963:G:A	NC_000001.11:154504963:G:A	(self)
ss41206143, ss97974811, ss106602089, ss138083209, ss143985741, ss155751990	NT_004487.19:5966081:G:A	NC_000001.11:154504963:G:A	(self)
ss18245980, ss20467881	NT_079484.1:927271:G:A	NC_000001.11:154504963:G:A	(self)
2389126, ss3895211732	NC_000001.10:154477439:G:C	NC_000001.11:154504963:G:C	(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 rs12118018

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

rs12118018