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dbSNP Short Genetic Variations

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.

rs3772173

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr3:170360444 (GRCh38.p12) 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
C=0.21159 (52003/245772, GnomAD)
C=0.28308 (35546/125568, TOPMED)
C=0.21972 (26649/121284, ExAC) (+ 6 more)
C=0.2696 (8332/30902, GnomAD)
C=0.2800 (3642/13006, GO-ESP)
C=0.310 (1551/5008, 1000G)
C=0.177 (794/4480, Estonian)
C=0.168 (647/3854, ALSPAC)
C=0.194 (721/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SKIL : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
Help

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.p12 chr 3 NC_000003.12:g.170360444C>T
GRCh37.p13 chr 3 NC_000003.11:g.170078232C>T
SKIL RefSeqGene NG_030357.1:g.7760C>T
Gene: SKIL, SKI like proto-oncogene (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SKIL transcript variant 1 NM_005414.4:c.113C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform 1 NP_005405.2:p.Ala38Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant 2 NM_001145097.2:c.113C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform 2 NP_001138569.1:p.Ala38Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant 3 NM_001145098.2:c.53C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform 3 NP_001138570.1:p.Ala18Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant 4 NM_001248008.1:c.113C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform 1 NP_001234937.1:p.Ala38Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant X1 XM_005247721.1:c.113C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform X1 XP_005247778.1:p.Ala38Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant X2 XM_006713735.1:c.113C>T A [GCA] > V [GTA] Coding Sequence Variant
ski-like protein isoform X1 XP_006713798.1:p.Ala38Val A (Ala) > V (Val) Missense Variant
SKIL transcript variant X3 XR_001740238.1:n.278C>T N/A Non Coding Transcript Variant
Help

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
Help

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
gnomAD - Exomes Global Study-wide 245772 C=0.21159 T=0.78841
gnomAD - Exomes European Sub 133784 C=0.17671 T=0.82329
gnomAD - Exomes Asian Sub 47932 C=0.2408 T=0.7592
gnomAD - Exomes American Sub 33504 C=0.1923 T=0.8077
gnomAD - Exomes African Sub 15284 C=0.4997 T=0.5003
gnomAD - Exomes Ashkenazi Jewish Sub 9806 C=0.169 T=0.831
gnomAD - Exomes Other Sub 5462 C=0.198 T=0.802
TopMed Global Study-wide 125568 C=0.28308 T=0.71692
ExAC Global Study-wide 121284 C=0.21972 T=0.78028
ExAC Europe Sub 73288 C=0.1770 T=0.8230
ExAC Asian Sub 25130 C=0.2433 T=0.7567
ExAC American Sub 11566 C=0.1872 T=0.8128
ExAC African Sub 10392 C=0.5013 T=0.4987
ExAC Other Sub 908 C=0.20 T=0.80
gnomAD - Genomes Global Study-wide 30902 C=0.2696 T=0.7304
gnomAD - Genomes European Sub 18498 C=0.1778 T=0.8222
gnomAD - Genomes African Sub 8676 C=0.500 T=0.500
gnomAD - Genomes East Asian Sub 1610 C=0.162 T=0.838
gnomAD - Genomes Other Sub 982 C=0.23 T=0.77
gnomAD - Genomes American Sub 834 C=0.21 T=0.79
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.18 T=0.82
GO Exome Sequencing Project Global Study-wide 13006 C=0.2800 T=0.7200
GO Exome Sequencing Project European American Sub 8600 C=0.180 T=0.820
GO Exome Sequencing Project African American Sub 4406 C=0.476 T=0.524
1000Genomes Global Study-wide 5008 C=0.310 T=0.690
1000Genomes African Sub 1322 C=0.572 T=0.428
1000Genomes East Asian Sub 1008 C=0.162 T=0.838
1000Genomes Europe Sub 1006 C=0.184 T=0.816
1000Genomes South Asian Sub 978 C=0.33 T=0.67
1000Genomes American Sub 694 C=0.18 T=0.82
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.177 T=0.823
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.168 T=0.832
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.194 T=0.806
Help

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 Note
GRCh38.p12 chr 3 NC_000003.12:g.170360444C= NC_000003.12:g.17036044...

NC_000003.12:g.170360444C>T

GRCh37.p13 chr 3 NC_000003.11:g.170078232C= NC_000003.11:g.17007823...

NC_000003.11:g.170078232C>T

SKIL RefSeqGene NG_030357.1:g.7760C= NG_030357.1:g.7760C>T
SKIL transcript variant 1 NM_005414.4:c.113C= NM_005414.4:c.113C>T
SKIL transcript variant 2 NM_001145097.2:c.113C= NM_001145097.2:c.113C>T
SKIL transcript variant 3 NM_001145098.2:c.53C= NM_001145098.2:c.53C>T
SKIL transcript variant 4 NM_001248008.1:c.113C= NM_001248008.1:c.113C>T
SKIL transcript variant X2 XM_006713735.1:c.113C= XM_006713735.1:c.113C>T
SKIL transcript variant X1 XM_005247721.1:c.113C= XM_005247721.1:c.113C>T
SKIL transcript variant X3 XR_001740238.1:n.278C= XR_001740238.1:n.278C>T
ski-like protein isoform 1 NP_005405.2:p.Ala38= NP_005405.2:p.Ala38Val
ski-like protein isoform 2 NP_001138569.1:p.Ala38= NP_001138569.1:p.Ala38Val
ski-like protein isoform 3 NP_001138570.1:p.Ala18= NP_001138570.1:p.Ala18Val
ski-like protein isoform 1 NP_001234937.1:p.Ala38= NP_001234937.1:p.Ala38Val
ski-like protein isoform X1 XP_006713798.1:p.Ala38= XP_006713798.1:p.Ala38Val
ski-like protein isoform X1 XP_005247778.1:p.Ala38= XP_005247778.1:p.Ala38Val
Help

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#.

117 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4958234 Aug 28, 2002 (107)
2 BCM_SSAHASNP ss10073365 Jul 11, 2003 (116)
3 MGC_GENOME_DIFF ss28498958 Sep 24, 2004 (126)
4 MGC_GENOME_DIFF ss28513956 Sep 24, 2004 (126)
5 ABI ss44448692 Mar 11, 2006 (126)
6 APPLERA_GI ss48413261 Mar 11, 2006 (126)
7 PERLEGEN ss68882284 May 17, 2007 (127)
8 AFFY ss74811674 Aug 16, 2007 (128)
9 ILLUMINA ss74895163 Dec 06, 2007 (129)
10 HGSV ss83817440 Dec 15, 2007 (130)
11 HGSV ss84664708 Dec 15, 2007 (130)
12 HGSV ss85911729 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss92368152 Mar 24, 2008 (129)
14 HUMANGENOME_JCVI ss96074451 Feb 05, 2009 (130)
15 BGI ss104011912 Dec 01, 2009 (131)
16 1000GENOMES ss111336300 Jan 25, 2009 (130)
17 1000GENOMES ss112685679 Jan 25, 2009 (130)
18 ILLUMINA-UK ss117374982 Feb 14, 2009 (130)
19 ILLUMINA ss120037302 Dec 01, 2009 (131)
20 ENSEMBL ss135430735 Dec 01, 2009 (131)
21 ENSEMBL ss139288884 Dec 01, 2009 (131)
22 GMI ss156494595 Dec 01, 2009 (131)
23 SEATTLESEQ ss159706515 Dec 01, 2009 (131)
24 ILLUMINA ss160639693 Dec 01, 2009 (131)
25 COMPLETE_GENOMICS ss162818947 Jul 04, 2010 (132)
26 COMPLETE_GENOMICS ss164950741 Jul 04, 2010 (132)
27 COMPLETE_GENOMICS ss167429559 Jul 04, 2010 (132)
28 ILLUMINA ss173633205 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss206077984 Jul 04, 2010 (132)
30 1000GENOMES ss220574220 Jul 14, 2010 (132)
31 1000GENOMES ss232139487 Jul 14, 2010 (132)
32 1000GENOMES ss239487867 Jul 15, 2010 (132)
33 ILLUMINA ss244296841 Jul 04, 2010 (132)
34 BL ss253678438 May 09, 2011 (134)
35 GMI ss277453493 May 04, 2012 (137)
36 GMI ss284793559 Apr 25, 2013 (138)
37 PJP ss292972463 May 09, 2011 (134)
38 NHLBI-ESP ss342151994 May 09, 2011 (134)
39 ILLUMINA ss480826564 May 04, 2012 (137)
40 ILLUMINA ss480842455 May 04, 2012 (137)
41 ILLUMINA ss481773497 Sep 08, 2015 (146)
42 ILLUMINA ss485208068 May 04, 2012 (137)
43 1000GENOMES ss490877830 May 04, 2012 (137)
44 EXOME_CHIP ss491348843 May 04, 2012 (137)
45 CLINSEQ_SNP ss491845358 May 04, 2012 (137)
46 ILLUMINA ss537192241 Sep 08, 2015 (146)
47 TISHKOFF ss557109862 Apr 25, 2013 (138)
48 SSMP ss650855524 Apr 25, 2013 (138)
49 ILLUMINA ss778523352 Sep 08, 2015 (146)
50 ILLUMINA ss780823999 Sep 08, 2015 (146)
51 ILLUMINA ss783050025 Sep 08, 2015 (146)
52 ILLUMINA ss783506561 Sep 08, 2015 (146)
53 ILLUMINA ss784008610 Sep 08, 2015 (146)
54 ILLUMINA ss832307865 Sep 08, 2015 (146)
55 ILLUMINA ss833979790 Sep 08, 2015 (146)
56 JMKIDD_LAB ss974450655 Aug 21, 2014 (142)
57 EVA-GONL ss979446117 Aug 21, 2014 (142)
58 JMKIDD_LAB ss1067456939 Aug 21, 2014 (142)
59 JMKIDD_LAB ss1071046909 Aug 21, 2014 (142)
60 1000GENOMES ss1307236669 Aug 21, 2014 (142)
61 HAMMER_LAB ss1397358852 Sep 08, 2015 (146)
62 DDI ss1429668922 Apr 01, 2015 (144)
63 EVA_GENOME_DK ss1580292940 Apr 01, 2015 (144)
64 EVA_FINRISK ss1584031546 Apr 01, 2015 (144)
65 EVA_DECODE ss1588940690 Apr 01, 2015 (144)
66 EVA_UK10K_ALSPAC ss1608785544 Apr 01, 2015 (144)
67 EVA_UK10K_TWINSUK ss1651779577 Apr 01, 2015 (144)
68 EVA_EXAC ss1687290552 Apr 01, 2015 (144)
69 EVA_MGP ss1711041009 Apr 01, 2015 (144)
70 EVA_SVP ss1712630918 Apr 01, 2015 (144)
71 ILLUMINA ss1752452071 Sep 08, 2015 (146)
72 ILLUMINA ss1752452072 Sep 08, 2015 (146)
73 HAMMER_LAB ss1800421763 Sep 08, 2015 (146)
74 ILLUMINA ss1917775026 Feb 12, 2016 (147)
75 WEILL_CORNELL_DGM ss1922666646 Feb 12, 2016 (147)
76 ILLUMINA ss1946102130 Feb 12, 2016 (147)
77 ILLUMINA ss1946102131 Feb 12, 2016 (147)
78 ILLUMINA ss1958627804 Feb 12, 2016 (147)
79 ILLUMINA ss1958627805 Feb 12, 2016 (147)
80 GENOMED ss1969587673 Jul 19, 2016 (147)
81 JJLAB ss2021908953 Sep 14, 2016 (149)
82 USC_VALOUEV ss2150006243 Dec 20, 2016 (150)
83 HUMAN_LONGEVITY ss2258088237 Dec 20, 2016 (150)
84 TOPMED ss2425482743 Dec 20, 2016 (150)
85 SYSTEMSBIOZJU ss2625454216 Nov 08, 2017 (151)
86 ILLUMINA ss2634042488 Nov 08, 2017 (151)
87 ILLUMINA ss2635127557 Nov 08, 2017 (151)
88 GRF ss2705426475 Nov 08, 2017 (151)
89 ILLUMINA ss2710991914 Nov 08, 2017 (151)
90 GNOMAD ss2734195955 Nov 08, 2017 (151)
91 GNOMAD ss2747138267 Nov 08, 2017 (151)
92 GNOMAD ss2802231749 Nov 08, 2017 (151)
93 AFFY ss2985276241 Nov 08, 2017 (151)
94 SWEGEN ss2993628526 Nov 08, 2017 (151)
95 BIOINF_KMB_FNS_UNIBA ss3024722660 Nov 08, 2017 (151)
96 CSHL ss3345391604 Nov 08, 2017 (151)
97 TOPMED ss3412648781 Nov 08, 2017 (151)
98 ILLUMINA ss3625831209 Oct 12, 2018 (152)
99 ILLUMINA ss3628833313 Oct 12, 2018 (152)
100 ILLUMINA ss3628833314 Oct 12, 2018 (152)
101 ILLUMINA ss3631983790 Oct 12, 2018 (152)
102 ILLUMINA ss3633316679 Oct 12, 2018 (152)
103 ILLUMINA ss3634034753 Oct 12, 2018 (152)
104 ILLUMINA ss3634927810 Oct 12, 2018 (152)
105 ILLUMINA ss3634927811 Oct 12, 2018 (152)
106 ILLUMINA ss3635718138 Oct 12, 2018 (152)
107 ILLUMINA ss3636625721 Oct 12, 2018 (152)
108 ILLUMINA ss3637470578 Oct 12, 2018 (152)
109 ILLUMINA ss3638455841 Oct 12, 2018 (152)
110 ILLUMINA ss3640635107 Oct 12, 2018 (152)
111 ILLUMINA ss3640635108 Oct 12, 2018 (152)
112 ILLUMINA ss3643409612 Oct 12, 2018 (152)
113 ILLUMINA ss3644834789 Oct 12, 2018 (152)
114 ILLUMINA ss3644834790 Oct 12, 2018 (152)
115 OMUKHERJEE_ADBS ss3646295606 Oct 12, 2018 (152)
116 URBANLAB ss3647584322 Oct 12, 2018 (152)
117 ILLUMINA ss3654046150 Oct 12, 2018 (152)
118 1000Genomes NC_000003.11 - 170078232 Oct 12, 2018 (152)
119 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 170078232 Oct 12, 2018 (152)
120 Genetic variation in the Estonian population NC_000003.11 - 170078232 Oct 12, 2018 (152)
121 ExAC NC_000003.11 - 170078232 Oct 12, 2018 (152)
122 gnomAD - Genomes NC_000003.11 - 170078232 Oct 12, 2018 (152)
123 gnomAD - Exomes NC_000003.11 - 170078232 Oct 12, 2018 (152)
124 GO Exome Sequencing Project NC_000003.11 - 170078232 Oct 12, 2018 (152)
125 TopMed NC_000003.12 - 170360444 Oct 12, 2018 (152)
126 UK 10K study - Twins NC_000003.11 - 170078232 Oct 12, 2018 (152)
Help

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)
rs17846573 Mar 11, 2006 (126)
rs17859654 Mar 11, 2006 (126)
rs52824578 Sep 21, 2007 (128)
rs58946182 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss83817440, ss84664708, ss85911729 NC_000003.9:171560933:C:T NC_000003.12:170360443:C:T (self)
ss92368152, ss111336300, ss112685679, ss117374982, ss162818947, ss164950741, ss167429559, ss206077984, ss253678438, ss277453493, ss284793559, ss292972463, ss480826564, ss491845358, ss1397358852, ss1588940690, ss1712630918, ss2635127557, ss3643409612 NC_000003.10:171560925:C:T NC_000003.12:170360443:C:T (self)
18541416, 10330850, 7314563, 7237113, 142859503, 2618517, 431873, 10330850, ss220574220, ss232139487, ss239487867, ss342151994, ss480842455, ss481773497, ss485208068, ss490877830, ss491348843, ss537192241, ss557109862, ss650855524, ss778523352, ss780823999, ss783050025, ss783506561, ss784008610, ss832307865, ss833979790, ss974450655, ss979446117, ss1067456939, ss1071046909, ss1307236669, ss1429668922, ss1580292940, ss1584031546, ss1608785544, ss1651779577, ss1687290552, ss1711041009, ss1752452071, ss1752452072, ss1800421763, ss1917775026, ss1922666646, ss1946102130, ss1946102131, ss1958627804, ss1958627805, ss1969587673, ss2021908953, ss2150006243, ss2425482743, ss2625454216, ss2634042488, ss2705426475, ss2710991914, ss2734195955, ss2747138267, ss2802231749, ss2985276241, ss2993628526, ss3345391604, ss3625831209, ss3628833313, ss3628833314, ss3631983790, ss3633316679, ss3634034753, ss3634927810, ss3634927811, ss3635718138, ss3636625721, ss3637470578, ss3638455841, ss3640635107, ss3640635108, ss3644834789, ss3644834790, ss3646295606, ss3654046150 NC_000003.11:170078231:C:T NC_000003.12:170360443:C:T (self)
269061626, ss2258088237, ss3024722660, ss3412648781, ss3647584322 NC_000003.12:170360443:C:T NC_000003.12:170360443:C:T (self)
ss4958234, ss28498958, ss28513956, ss44448692, ss48413261, ss68882284, ss74811674, ss74895163, ss96074451, ss104011912, ss120037302, ss135430735, ss139288884, ss156494595, ss159706515, ss160639693, ss173633205, ss244296841 NT_005612.16:76573377:C:T NC_000003.12:170360443:C:T (self)
ss10073365 NT_005962.15:5290694:C:T NC_000003.12:170360443:C:T (self)
Help

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

1 citation for rs3772173
PMID Title Author Year Journal
25668194 Examination of candidate exonic variants for association to Alzheimer disease in the Amish. D'Aoust LN et al. 2015 PloS one

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.

Software version is: 2.0.1.post104+4a6ee9c