Name: rs10070161
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.

rs10070161

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:71651046 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.213200 (56432/264690, TOPMED)
T=0.210640 (29490/140002, GnomAD)
T=0.04158 (1175/28258, 14KJPN) (+ 14 more)
T=0.17792 (3361/18890, ALFA)
T=0.04224 (708/16760, 8.3KJPN)
T=0.1933 (1238/6404, 1000G_30x)
T=0.1843 (923/5008, 1000G)
T=0.1453 (651/4480, Estonian)
T=0.1282 (494/3854, ALSPAC)
T=0.1351 (501/3708, TWINSUK)
T=0.0195 (57/2930, KOREAN)
T=0.144 (144/998, GoNL)
T=0.125 (75/600, NorthernSweden)
T=0.093 (50/536, SGDP_PRJ)
T=0.120 (26/216, Qatari)
T=0.07 (4/54, Siberian)
T=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MCCC2 : 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	T=0.17792	C=0.82208
European	Sub	14286	T=0.13531	C=0.86469
African	Sub	2946	T=0.4039	C=0.5961
African Others	Sub	114	T=0.430	C=0.570
African American	Sub	2832	T=0.4029	C=0.5971
Asian	Sub	112	T=0.000	C=1.000
East Asian	Sub	86	T=0.00	C=1.00
Other Asian	Sub	26	T=0.00	C=1.00
Latin American 1	Sub	146	T=0.199	C=0.801
Latin American 2	Sub	610	T=0.111	C=0.889
South Asian	Sub	98	T=0.07	C=0.93
Other	Sub	692	T=0.194	C=0.806

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=0.213200	C=0.786800
gnomAD - Genomes	Global	Study-wide	140002	T=0.210640	C=0.789360
gnomAD - Genomes	European	Sub	75870	T=0.13057	C=0.86943
gnomAD - Genomes	African	Sub	41910	T=0.40494	C=0.59506
gnomAD - Genomes	American	Sub	13636	T=0.13582	C=0.86418
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0918	C=0.9082
gnomAD - Genomes	East Asian	Sub	3122	T=0.0160	C=0.9840
gnomAD - Genomes	Other	Sub	2140	T=0.1897	C=0.8103
14KJPN	JAPANESE	Study-wide	28258	T=0.04158	C=0.95842
Allele Frequency Aggregator	Total	Global	18890	T=0.17792	C=0.82208
Allele Frequency Aggregator	European	Sub	14286	T=0.13531	C=0.86469
Allele Frequency Aggregator	African	Sub	2946	T=0.4039	C=0.5961
Allele Frequency Aggregator	Other	Sub	692	T=0.194	C=0.806
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.111	C=0.889
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.199	C=0.801
Allele Frequency Aggregator	Asian	Sub	112	T=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.07	C=0.93
8.3KJPN	JAPANESE	Study-wide	16760	T=0.04224	C=0.95776
1000Genomes_30x	Global	Study-wide	6404	T=0.1933	C=0.8067
1000Genomes_30x	African	Sub	1786	T=0.4614	C=0.5386
1000Genomes_30x	Europe	Sub	1266	T=0.1548	C=0.8452
1000Genomes_30x	South Asian	Sub	1202	T=0.0591	C=0.9409
1000Genomes_30x	East Asian	Sub	1170	T=0.0205	C=0.9795
1000Genomes_30x	American	Sub	980	T=0.126	C=0.874
1000Genomes	Global	Study-wide	5008	T=0.1843	C=0.8157
1000Genomes	African	Sub	1322	T=0.4546	C=0.5454
1000Genomes	East Asian	Sub	1008	T=0.0198	C=0.9802
1000Genomes	Europe	Sub	1006	T=0.1521	C=0.8479
1000Genomes	South Asian	Sub	978	T=0.057	C=0.943
1000Genomes	American	Sub	694	T=0.134	C=0.866
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1453	C=0.8547
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1282	C=0.8718
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1351	C=0.8649
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0195	A=0.0000, C=0.9805, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.144	C=0.856
Northern Sweden	ACPOP	Study-wide	600	T=0.125	C=0.875
SGDP_PRJ	Global	Study-wide	536	T=0.093	C=0.907
Qatari	Global	Study-wide	216	T=0.120	C=0.880
Siberian	Global	Study-wide	54	T=0.07	C=0.93
The Danish reference pan genome	Danish	Study-wide	40	T=0.15	C=0.85

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.71651046T>A
GRCh38.p14 chr 5	NC_000005.10:g.71651046T>C
GRCh38.p14 chr 5	NC_000005.10:g.71651046T>G
GRCh37.p13 chr 5	NC_000005.9:g.70946873T>A
GRCh37.p13 chr 5	NC_000005.9:g.70946873T>C
GRCh37.p13 chr 5	NC_000005.9:g.70946873T>G
MCCC2 RefSeqGene	NG_008882.1:g.68759T>A
MCCC2 RefSeqGene	NG_008882.1:g.68759T>C
MCCC2 RefSeqGene	NG_008882.1:g.68759T>G

Gene: MCCC2, methylcrotonyl-CoA carboxylase subunit 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MCCC2 transcript variant 2	NM_001363147.1:c.1374+863… NM_001363147.1:c.1374+863T>A	N/A	Intron Variant
MCCC2 transcript variant 1	NM_022132.5:c.1488+863T>A	N/A	Intron Variant
MCCC2 transcript variant X3	XM_011543529.3:c.	N/A	Genic Downstream Transcript Variant
MCCC2 transcript variant X2	XM_017009688.2:c.	N/A	Genic Downstream Transcript Variant
MCCC2 transcript variant X1	XM_047417468.1:c.	N/A	Genic Downstream Transcript Variant
MCCC2 transcript variant X4	XM_047417469.1:c.	N/A	Genic Downstream Transcript Variant
MCCC2 transcript variant X5	XM_047417470.1:c.	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	T=	A	C	G
GRCh38.p14 chr 5	NC_000005.10:g.71651046=	NC_000005.10:g.71651046T>A	NC_000005.10:g.71651046T>C	NC_000005.10:g.71651046T>G
GRCh37.p13 chr 5	NC_000005.9:g.70946873=	NC_000005.9:g.70946873T>A	NC_000005.9:g.70946873T>C	NC_000005.9:g.70946873T>G
MCCC2 RefSeqGene	NG_008882.1:g.68759=	NG_008882.1:g.68759T>A	NG_008882.1:g.68759T>C	NG_008882.1:g.68759T>G
MCCC2 transcript variant 2	NM_001363147.1:c.1374+863=	NM_001363147.1:c.1374+863T>A	NM_001363147.1:c.1374+863T>C	NM_001363147.1:c.1374+863T>G
MCCC2 transcript variant 1	NM_022132.4:c.1488+863=	NM_022132.4:c.1488+863T>A	NM_022132.4:c.1488+863T>C	NM_022132.4:c.1488+863T>G
MCCC2 transcript variant 1	NM_022132.5:c.1488+863=	NM_022132.5:c.1488+863T>A	NM_022132.5:c.1488+863T>C	NM_022132.5:c.1488+863T>G
MCCC2 transcript variant X1	XM_005248567.1:c.1374+863=	XM_005248567.1:c.1374+863T>A	XM_005248567.1:c.1374+863T>C	XM_005248567.1:c.1374+863T>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#.

69 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13922573	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss19636387	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss20249905	Feb 27, 2004 (120)
4	SSAHASNP	ss22264789	Apr 05, 2004 (121)
5	HGSV	ss79688361	Dec 15, 2007 (130)
6	HGSV	ss85140818	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss93131397	Mar 24, 2008 (129)
8	BGI	ss105930133	Feb 05, 2009 (130)
9	ENSEMBL	ss142618145	Dec 01, 2009 (131)
10	GMI	ss155565683	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss162344656	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss166668468	Jul 04, 2010 (132)
13	BUSHMAN	ss200368118	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss207078169	Jul 04, 2010 (132)
15	BL	ss253526797	May 09, 2011 (134)
16	GMI	ss278329923	May 04, 2012 (137)
17	GMI	ss285194993	Apr 25, 2013 (138)
18	PJP	ss293376936	May 09, 2011 (134)
19	1000GENOMES	ss332535510	May 09, 2011 (134)
20	TISHKOFF	ss558454974	Apr 25, 2013 (138)
21	SSMP	ss652325906	Apr 25, 2013 (138)
22	EVA-GONL	ss981673490	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1072708653	Aug 21, 2014 (142)
24	1000GENOMES	ss1315508412	Aug 21, 2014 (142)
25	DDI	ss1430375347	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1581179387	Apr 01, 2015 (144)
27	EVA_DECODE	ss1591192114	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1613104229	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1656098262	Apr 01, 2015 (144)
30	HAMMER_LAB	ss1803651287	Sep 08, 2015 (146)
31	WEILL_CORNELL_DGM	ss1924930707	Feb 12, 2016 (147)
32	GENOMED	ss1970111317	Jul 19, 2016 (147)
33	JJLAB	ss2023070035	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2151225633	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2274548604	Dec 20, 2016 (150)
36	SYSTEMSBIOZJU	ss2626031488	Nov 08, 2017 (151)
37	GRF	ss2706772558	Nov 08, 2017 (151)
38	SWEGEN	ss2997107095	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3025319153	Nov 08, 2017 (151)
40	CSHL	ss3346434497	Nov 08, 2017 (151)
41	URBANLAB	ss3648085835	Oct 12, 2018 (152)
42	EGCUT_WGS	ss3664982101	Jul 13, 2019 (153)
43	EVA_DECODE	ss3714884343	Jul 13, 2019 (153)
44	ACPOP	ss3732445434	Jul 13, 2019 (153)
45	EVA	ss3763553063	Jul 13, 2019 (153)
46	PACBIO	ss3785138869	Jul 13, 2019 (153)
47	PACBIO	ss3790540849	Jul 13, 2019 (153)
48	PACBIO	ss3795417409	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3806721662	Jul 13, 2019 (153)
50	EVA	ss3829295027	Apr 26, 2020 (154)
51	EVA	ss3838121310	Apr 26, 2020 (154)
52	EVA	ss3843562027	Apr 26, 2020 (154)
53	SGDP_PRJ	ss3862081326	Apr 26, 2020 (154)
54	KRGDB	ss3908641283	Apr 26, 2020 (154)
55	GNOMAD	ss4106312806	Apr 26, 2021 (155)
56	TOPMED	ss4663586912	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5172229579	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5264339881	Oct 13, 2022 (156)
59	HUGCELL_USP	ss5462476628	Oct 13, 2022 (156)
60	EVA	ss5508059860	Oct 13, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5548182764	Oct 13, 2022 (156)
62	SANFORD_IMAGENETICS	ss5638014516	Oct 13, 2022 (156)
63	TOMMO_GENOMICS	ss5708765409	Oct 13, 2022 (156)
64	YY_MCH	ss5806409456	Oct 13, 2022 (156)
65	EVA	ss5835067233	Oct 13, 2022 (156)
66	EVA	ss5854853459	Oct 13, 2022 (156)
67	EVA	ss5894595255	Oct 13, 2022 (156)
68	EVA	ss5966441625	Oct 13, 2022 (156)
69	EVA	ss5980299234	Oct 13, 2022 (156)
70	1000Genomes	NC_000005.9 - 70946873	Oct 12, 2018 (152)
71	1000Genomes_30x	NC_000005.10 - 71651046	Oct 13, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 70946873	Oct 12, 2018 (152)
73	Genetic variation in the Estonian population	NC_000005.9 - 70946873	Oct 12, 2018 (152)
74	The Danish reference pan genome	NC_000005.9 - 70946873	Apr 26, 2020 (154)
75	gnomAD - Genomes	NC_000005.10 - 71651046	Apr 26, 2021 (155)
76	Genome of the Netherlands Release 5	NC_000005.9 - 70946873	Apr 26, 2020 (154)
77	KOREAN population from KRGDB	NC_000005.9 - 70946873	Apr 26, 2020 (154)
78	Northern Sweden	NC_000005.9 - 70946873	Jul 13, 2019 (153)
79	Qatari	NC_000005.9 - 70946873	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000005.9 - 70946873	Apr 26, 2020 (154)
81	Siberian	NC_000005.9 - 70946873	Apr 26, 2020 (154)
82	8.3KJPN	NC_000005.9 - 70946873	Apr 26, 2021 (155)
83	14KJPN	NC_000005.10 - 71651046	Oct 13, 2022 (156)
84	TopMed	NC_000005.10 - 71651046	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000005.9 - 70946873	Oct 12, 2018 (152)
86	ALFA	NC_000005.10 - 71651046	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)
rs59994836	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
15818677, ss3908641283	NC_000005.9:70946872:T:A	NC_000005.10:71651045:T:A	(self)
ss79688361, ss85140818, ss93131397, ss162344656, ss166668468, ss200368118, ss207078169, ss253526797, ss278329923, ss285194993, ss293376936, ss1591192114	NC_000005.8:70982628:T:C	NC_000005.10:71651045:T:C	(self)
27123432, 15077722, 10720349, 7344326, 6703595, 15818677, 5730299, 6972637, 14098306, 3741987, 30198886, 15077722, ss332535510, ss558454974, ss652325906, ss981673490, ss1072708653, ss1315508412, ss1430375347, ss1581179387, ss1613104229, ss1656098262, ss1803651287, ss1924930707, ss1970111317, ss2023070035, ss2151225633, ss2626031488, ss2706772558, ss2997107095, ss3346434497, ss3664982101, ss3732445434, ss3763553063, ss3785138869, ss3790540849, ss3795417409, ss3829295027, ss3838121310, ss3862081326, ss3908641283, ss5172229579, ss5508059860, ss5638014516, ss5835067233, ss5966441625, ss5980299234	NC_000005.9:70946872:T:C	NC_000005.10:71651045:T:C	(self)
35708699, 191748195, 42602513, 500964469, 8601498788, ss2274548604, ss3025319153, ss3648085835, ss3714884343, ss3806721662, ss3843562027, ss4106312806, ss4663586912, ss5264339881, ss5462476628, ss5548182764, ss5708765409, ss5806409456, ss5854853459, ss5894595255	NC_000005.10:71651045:T:C	NC_000005.10:71651045:T:C	(self)
ss13922573, ss19636387, ss20249905, ss22264789	NT_006713.13:339004:T:C	NC_000005.10:71651045:T:C	(self)
ss105930133, ss142618145, ss155565683	NT_006713.15:21541231:T:C	NC_000005.10:71651045:T:C	(self)
15818677, ss3908641283	NC_000005.9:70946872:T:G	NC_000005.10:71651045:T:G	(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 rs10070161

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

rs10070161