Name: rs187029529
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.

rs187029529

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:75099104 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.000563 (149/264690, TOPMED)
C=0.01161 (328/28258, 14KJPN)
C=0.01205 (202/16760, 8.3KJPN) (+ 8 more)
A=0.00000 (0/14418, ALFA)
C=0.00000 (0/14418, ALFA)
C=0.0023 (15/6404, 1000G_30x)
C=0.0002 (1/6330, GnomAD_exome)
C=0.0018 (9/5008, 1000G)
C=0.0168 (49/2922, KOREAN)
C=0.0240 (44/1832, Korea1K)
C=0.0006 (1/1568, ExAC)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DUSP13 : Missense Variant
SAMD8 : 2KB Upstream 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	14418	T=1.00000	A=0.00000, C=0.00000
European	Sub	9824	T=1.0000	A=0.0000, C=0.0000
African	Sub	2946	T=1.0000	A=0.0000, C=0.0000
African Others	Sub	114	T=1.000	A=0.000, C=0.000
African American	Sub	2832	T=1.0000	A=0.0000, C=0.0000
Asian	Sub	110	T=1.000	A=0.000, C=0.000
East Asian	Sub	84	T=1.00	A=0.00, C=0.00
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	146	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	610	T=1.000	A=0.000, C=0.000
South Asian	Sub	98	T=1.00	A=0.00, C=0.00
Other	Sub	684	T=1.000	A=0.000, C=0.000

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=0.999437	C=0.000563
14KJPN	JAPANESE	Study-wide	28258	T=0.98839	C=0.01161
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98795	C=0.01205
Allele Frequency Aggregator	Total	Global	14418	T=1.00000	A=0.00000, C=0.00000
Allele Frequency Aggregator	European	Sub	9824	T=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	African	Sub	2946	T=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	Other	Sub	684	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	110	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9977	C=0.0023
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.9872	C=0.0128
1000Genomes_30x	American	Sub	980	T=1.000	C=0.000
gnomAD - Exomes	Global	Study-wide	6330	T=0.9998	C=0.0002
gnomAD - Exomes	European	Sub	5330	T=1.0000	C=0.0000
gnomAD - Exomes	African	Sub	352	T=1.000	C=0.000
gnomAD - Exomes	Ashkenazi Jewish	Sub	204	T=1.000	C=0.000
gnomAD - Exomes	Asian	Sub	180	T=0.994	C=0.006
gnomAD - Exomes	Other	Sub	146	T=1.000	C=0.000
gnomAD - Exomes	American	Sub	118	T=1.000	C=0.000
1000Genomes	Global	Study-wide	5008	T=0.9982	C=0.0018
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9911	C=0.0089
1000Genomes	Europe	Sub	1006	T=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=1.000	C=0.000
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9832	C=0.0168
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9760	C=0.0240
ExAC	Global	Study-wide	1568	T=0.9994	C=0.0006
ExAC	Europe	Sub	906	T=1.000	C=0.000
ExAC	African	Sub	372	T=1.000	C=0.000
ExAC	Asian	Sub	180	T=0.994	C=0.006
ExAC	American	Sub	96	T=1.00	C=0.00
ExAC	Other	Sub	14	T=1.00	C=0.00

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 10	NC_000010.11:g.75099104T>A
GRCh38.p14 chr 10	NC_000010.11:g.75099104T>C
GRCh37.p13 chr 10	NC_000010.10:g.76858862T>A
GRCh37.p13 chr 10	NC_000010.10:g.76858862T>C
DUSP13B RefSeqGene	NG_033976.1:g.15109A>T
DUSP13B RefSeqGene	NG_033976.1:g.15109A>G

Gene: DUSP13, dual specificity phosphatase 13 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DUSP13 transcript variant 1	NM_001007271.2:c.308-121… NM_001007271.2:c.308-1219A>T	N/A	Intron Variant
DUSP13B transcript variant 2	NM_001007272.2:c.150-1219… NM_001007272.2:c.150-1219A>T	N/A	Intron Variant
DUSP13B transcript variant 3	NM_001007273.2:c.279-1219… NM_001007273.2:c.279-1219A>T	N/A	Intron Variant
DUSP13B transcript variant 7	NM_001320842.2:c.279-1219… NM_001320842.2:c.279-1219A>T	N/A	Intron Variant
DUSP13B transcript variant 8	NM_001320843.2:c.-1-1219A… NM_001320843.2:c.-1-1219A>T	N/A	Intron Variant
DUSP13B transcript variant 6	NM_016364.3:c.-2+325A>T	N/A	Intron Variant
DUSP13B transcript variant 9	NM_001363514.2:c.334A>T	S [AGC] > C [TGC]	Coding Sequence Variant
dual specificity protein phosphatase 13B isoform 9	NP_001350443.1:p.Ser112Cys	S (Ser) > C (Cys)	Missense Variant
DUSP13B transcript variant 9	NM_001363514.2:c.334A>G	S [AGC] > G [GGC]	Coding Sequence Variant
dual specificity protein phosphatase 13B isoform 9	NP_001350443.1:p.Ser112Gly	S (Ser) > G (Gly)	Missense Variant
DUSP13 transcript variant X1	XM_005269883.4:c.657-1219… XM_005269883.4:c.657-1219A>T	N/A	Intron Variant
DUSP13 transcript variant X4	XM_011539855.3:c.-2+226A>T	N/A	Intron Variant
DUSP13 transcript variant X3	XM_047425305.1:c.-1-1219A… XM_047425305.1:c.-1-1219A>T	N/A	Intron Variant
DUSP13 transcript variant X5	XM_047425306.1:c.-1-1219A… XM_047425306.1:c.-1-1219A>T	N/A	Intron Variant
DUSP13 transcript variant X6	XM_047425308.1:c.-1-1219A… XM_047425308.1:c.-1-1219A>T	N/A	Intron Variant
DUSP13 transcript variant X2	XM_017016314.2:c.	N/A	Genic Downstream Transcript Variant

Gene: SAMD8, sterile alpha motif domain containing 8 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SAMD8 transcript variant 1	NM_001174156.2:c.	N/A	N/A
SAMD8 transcript variant 2	NM_144660.3:c.	N/A	N/A
SAMD8 transcript variant X4	XM_011539312.4:c.	N/A	Upstream Transcript Variant
SAMD8 transcript variant X2	XM_005269541.6:c.	N/A	N/A
SAMD8 transcript variant X1	XM_017015738.3:c.	N/A	N/A
SAMD8 transcript variant X3	XM_047424640.1:c.	N/A	N/A
SAMD8 transcript variant X5	XM_047424641.1:c.	N/A	N/A

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=	A	C
GRCh38.p14 chr 10	NC_000010.11:g.75099104=	NC_000010.11:g.75099104T>A	NC_000010.11:g.75099104T>C
GRCh37.p13 chr 10	NC_000010.10:g.76858862=	NC_000010.10:g.76858862T>A	NC_000010.10:g.76858862T>C
DUSP13B RefSeqGene	NG_033976.1:g.15109=	NG_033976.1:g.15109A>T	NG_033976.1:g.15109A>G
DUSP13B transcript variant 9	NM_001363514.2:c.334=	NM_001363514.2:c.334A>T	NM_001363514.2:c.334A>G
DUSP13 transcript variant 9	NM_001363514.1:c.334=	NM_001363514.1:c.334A>T	NM_001363514.1:c.334A>G
dual specificity protein phosphatase 13B isoform 9	NP_001350443.1:p.Ser112=	NP_001350443.1:p.Ser112Cys	NP_001350443.1:p.Ser112Gly
DUSP13 transcript variant 1	NM_001007271.1:c.*308-1219=	NM_001007271.1:c.*308-1219A>T	NM_001007271.1:c.*308-1219A>G
DUSP13 transcript variant 1	NM_001007271.2:c.*308-1219=	NM_001007271.2:c.*308-1219A>T	NM_001007271.2:c.*308-1219A>G
DUSP13 transcript variant 2	NM_001007272.1:c.150-1219=	NM_001007272.1:c.150-1219A>T	NM_001007272.1:c.150-1219A>G
DUSP13B transcript variant 2	NM_001007272.2:c.150-1219=	NM_001007272.2:c.150-1219A>T	NM_001007272.2:c.150-1219A>G
DUSP13 transcript variant 3	NM_001007273.1:c.279-1219=	NM_001007273.1:c.279-1219A>T	NM_001007273.1:c.279-1219A>G
DUSP13B transcript variant 3	NM_001007273.2:c.279-1219=	NM_001007273.2:c.279-1219A>T	NM_001007273.2:c.279-1219A>G
DUSP13B transcript variant 7	NM_001320842.2:c.279-1219=	NM_001320842.2:c.279-1219A>T	NM_001320842.2:c.279-1219A>G
DUSP13B transcript variant 8	NM_001320843.2:c.-1-1219=	NM_001320843.2:c.-1-1219A>T	NM_001320843.2:c.-1-1219A>G
DUSP13B transcript variant 6	NM_016364.3:c.-2+325=	NM_016364.3:c.-2+325A>T	NM_016364.3:c.-2+325A>G
DUSP13 transcript variant X1	XM_005269883.1:c.657-1219=	XM_005269883.1:c.657-1219A>T	XM_005269883.1:c.657-1219A>G
DUSP13 transcript variant X1	XM_005269883.4:c.657-1219=	XM_005269883.4:c.657-1219A>T	XM_005269883.4:c.657-1219A>G
DUSP13 transcript variant X3	XM_005269885.1:c.387-1219=	XM_005269885.1:c.387-1219A>T	XM_005269885.1:c.387-1219A>G
DUSP13 transcript variant X4	XM_005269886.1:c.279-1219=	XM_005269886.1:c.279-1219A>T	XM_005269886.1:c.279-1219A>G
DUSP13 transcript variant X4	XM_005269887.1:c.279-1219=	XM_005269887.1:c.279-1219A>T	XM_005269887.1:c.279-1219A>G
DUSP13 transcript variant X7	XM_005269888.1:c.-1-1219=	XM_005269888.1:c.-1-1219A>T	XM_005269888.1:c.-1-1219A>G
DUSP13 transcript variant X7	XM_005269889.1:c.-1-1219=	XM_005269889.1:c.-1-1219A>T	XM_005269889.1:c.-1-1219A>G
DUSP13 transcript variant X10	XM_005269890.1:c.-1-1219=	XM_005269890.1:c.-1-1219A>T	XM_005269890.1:c.-1-1219A>G
DUSP13 transcript variant X4	XM_011539855.3:c.-2+226=	XM_011539855.3:c.-2+226A>T	XM_011539855.3:c.-2+226A>G
DUSP13 transcript variant X3	XM_047425305.1:c.-1-1219=	XM_047425305.1:c.-1-1219A>T	XM_047425305.1:c.-1-1219A>G
DUSP13 transcript variant X5	XM_047425306.1:c.-1-1219=	XM_047425306.1:c.-1-1219A>T	XM_047425306.1:c.-1-1219A>G
DUSP13 transcript variant X6	XM_047425308.1:c.-1-1219=	XM_047425308.1:c.-1-1219A>T	XM_047425308.1:c.-1-1219A>G

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#.

23 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss461731009	Sep 17, 2011 (135)
2	SSMP	ss656981941	Apr 25, 2013 (138)
3	1000GENOMES	ss1338072597	Aug 21, 2014 (142)
4	EVA_EXAC	ss1689964079	Apr 01, 2015 (144)
5	HUMAN_LONGEVITY	ss2176052759	Dec 20, 2016 (150)
6	GRF	ss2698759552	Nov 08, 2017 (151)
7	GNOMAD	ss2738344950	Nov 08, 2017 (151)
8	GNOMAD	ss2748418591	Nov 08, 2017 (151)
9	GNOMAD	ss2890568605	Nov 08, 2017 (151)
10	EVA	ss3748295620	Jul 13, 2019 (153)
11	KHV_HUMAN_GENOMES	ss3813668262	Jul 13, 2019 (153)
12	KRGDB	ss3922637633	Apr 26, 2020 (154)
13	KOGIC	ss3968193154	Apr 26, 2020 (154)
14	TOPMED	ss4857864409	Apr 26, 2021 (155)
15	TOMMO_GENOMICS	ss5198349928	Apr 26, 2021 (155)
16	1000G_HIGH_COVERAGE	ss5284608713	Oct 16, 2022 (156)
17	EVA	ss5394454859	Oct 16, 2022 (156)
18	HUGCELL_USP	ss5480128029	Oct 16, 2022 (156)
19	1000G_HIGH_COVERAGE	ss5578833965	Oct 16, 2022 (156)
20	TOMMO_GENOMICS	ss5744391110	Oct 16, 2022 (156)
21	YY_MCH	ss5811671003	Oct 16, 2022 (156)
22	EVA	ss5879540587	Oct 16, 2022 (156)
23	EVA	ss5940886495	Oct 16, 2022 (156)
24	1000Genomes	NC_000010.10 - 76858862	Oct 12, 2018 (152)
25	1000Genomes_30x	NC_000010.11 - 75099104	Oct 16, 2022 (156)
26	ExAC	NC_000010.10 - 76858862	Oct 12, 2018 (152)
27	gnomAD - Genomes Submission ignored due to conflicting rows: Row 356780373 (NC_000010.11:75099103:T:A 1/140254) Row 356780374 (NC_000010.11:75099103:T:C 42/140254)	-	Apr 26, 2021 (155)
28	gnomAD - Genomes Submission ignored due to conflicting rows: Row 356780373 (NC_000010.11:75099103:T:A 1/140254) Row 356780374 (NC_000010.11:75099103:T:C 42/140254)	-	Apr 26, 2021 (155)
29	gnomAD - Exomes	NC_000010.10 - 76858862	Jul 13, 2019 (153)
30	KOREAN population from KRGDB	NC_000010.10 - 76858862	Apr 26, 2020 (154)
31	Korean Genome Project	NC_000010.11 - 75099104	Apr 26, 2020 (154)
32	8.3KJPN	NC_000010.10 - 76858862	Apr 26, 2021 (155)
33	14KJPN	NC_000010.11 - 75099104	Oct 16, 2022 (156)
34	TopMed	NC_000010.11 - 75099104	Apr 26, 2021 (155)
35	ALFA	NC_000010.11 - 75099104	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
7054623479, ss2176052759, ss5480128029	NC_000010.11:75099103:T:A	NC_000010.11:75099103:T:A	(self)
50484355, 189863, 7543787, 29815027, 56319235, ss461731009, ss656981941, ss1338072597, ss1689964079, ss2698759552, ss2738344950, ss2748418591, ss2890568605, ss3748295620, ss3922637633, ss5198349928, ss5394454859, ss5940886495	NC_000010.10:76858861:T:C	NC_000010.11:75099103:T:C	(self)
66359900, 24571155, 78228214, 73410064, 7054623479, ss2176052759, ss3813668262, ss3968193154, ss4857864409, ss5284608713, ss5578833965, ss5744391110, ss5811671003, ss5879540587	NC_000010.11:75099103:T:C	NC_000010.11:75099103:T: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 rs187029529

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

rs187029529