Name: rs3031505
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.

rs3031505

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:29495056-29495060 (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: delAAACT
Variation Type: Deletion
Frequency: delAAACT=0.224251 (25988/115888, GnomAD_exome)
delAAACT=0.11032 (5683/51514, ExAC)
AAACT=0.28211 (7972/28258, 14KJPN) (+ 5 more)
AAACT=0.25734 (4313/16760, 8.3KJPN)
AAACT=0.25862 (4243/16406, ALFA)
delAAACT=0.24254 (2844/11726, GO-ESP)
AAACT=0.2889 (1850/6404, 1000G_30x)
AAACT=0.4696 (2352/5008, 1000G)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SVIL : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	16406	AAACT=0.25862	=0.74138	0.001463	0.484213	0.514324	32
European	Sub	12130	AAACT=0.26744	=0.73256	0.0	0.465128	0.534872	32
African	Sub	2830	AAACT=0.2350	=0.7650	0.008481	0.538516	0.453004	32
African Others	Sub	108	AAACT=0.231	=0.769	0.0	0.537037	0.462963	3
African American	Sub	2722	AAACT=0.2351	=0.7649	0.008817	0.538575	0.452608	32
Asian	Sub	108	AAACT=0.241	=0.759	0.0	0.518519	0.481481	3
East Asian	Sub	84	AAACT=0.21	=0.79	0.0	0.571429	0.428571	2
Other Asian	Sub	24	AAACT=0.33	=0.67	0.0	0.333333	0.666667	2
Latin American 1	Sub	146	AAACT=0.315	=0.685	0.0	0.369863	0.630137	9
Latin American 2	Sub	610	AAACT=0.195	=0.805	0.0	0.609836	0.390164	10
South Asian	Sub	94	AAACT=0.34	=0.66	0.0	0.319149	0.680851	7
Other	Sub	488	AAACT=0.227	=0.773	0.0	0.545082	0.454918	12

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	115888	AAACT=0.775749	delAAACT=0.224251
gnomAD - Exomes	European	Sub	63722	AAACT=0.83812	delAAACT=0.16188
gnomAD - Exomes	Asian	Sub	23756	AAACT=0.68833	delAAACT=0.31167
gnomAD - Exomes	American	Sub	12908	AAACT=0.65641	delAAACT=0.34359
gnomAD - Exomes	African	Sub	8024	AAACT=0.7238	delAAACT=0.2762
gnomAD - Exomes	Ashkenazi Jewish	Sub	4430	AAACT=0.8318	delAAACT=0.1682
gnomAD - Exomes	Other	Sub	3048	AAACT=0.7136	delAAACT=0.2864
ExAC	Global	Study-wide	51514	AAACT=0.88968	delAAACT=0.11032
ExAC	Europe	Sub	31228	AAACT=0.90163	delAAACT=0.09837
ExAC	Asian	Sub	11798	AAACT=0.85413	delAAACT=0.14587
ExAC	African	Sub	4754	AAACT=0.8925	delAAACT=0.1075
ExAC	American	Sub	3386	AAACT=0.9019	delAAACT=0.0981
ExAC	Other	Sub	348	AAACT=0.865	delAAACT=0.135
14KJPN	JAPANESE	Study-wide	28258	AAACT=0.28211	delAAACT=0.71789
8.3KJPN	JAPANESE	Study-wide	16760	AAACT=0.25734	delAAACT=0.74266
Allele Frequency Aggregator	Total	Global	16406	AAACT=0.25862	delAAACT=0.74138
Allele Frequency Aggregator	European	Sub	12130	AAACT=0.26744	delAAACT=0.73256
Allele Frequency Aggregator	African	Sub	2830	AAACT=0.2350	delAAACT=0.7650
Allele Frequency Aggregator	Latin American 2	Sub	610	AAACT=0.195	delAAACT=0.805
Allele Frequency Aggregator	Other	Sub	488	AAACT=0.227	delAAACT=0.773
Allele Frequency Aggregator	Latin American 1	Sub	146	AAACT=0.315	delAAACT=0.685
Allele Frequency Aggregator	Asian	Sub	108	AAACT=0.241	delAAACT=0.759
Allele Frequency Aggregator	South Asian	Sub	94	AAACT=0.34	delAAACT=0.66
GO Exome Sequencing Project	Global	Study-wide	11726	AAACT=0.75746	delAAACT=0.24254
GO Exome Sequencing Project	European American	Sub	7830	AAACT=0.7741	delAAACT=0.2259
GO Exome Sequencing Project	African American	Sub	3896	AAACT=0.7241	delAAACT=0.2759
1000Genomes_30x	Global	Study-wide	6404	AAACT=0.2889	delAAACT=0.7111
1000Genomes_30x	African	Sub	1786	AAACT=0.2620	delAAACT=0.7380
1000Genomes_30x	Europe	Sub	1266	AAACT=0.2899	delAAACT=0.7101
1000Genomes_30x	South Asian	Sub	1202	AAACT=0.3602	delAAACT=0.6398
1000Genomes_30x	East Asian	Sub	1170	AAACT=0.2718	delAAACT=0.7282
1000Genomes_30x	American	Sub	980	AAACT=0.269	delAAACT=0.731
1000Genomes	Global	Study-wide	5008	AAACT=0.4696	delAAACT=0.5304
1000Genomes	African	Sub	1322	AAACT=0.4365	delAAACT=0.5635
1000Genomes	East Asian	Sub	1008	AAACT=0.3720	delAAACT=0.6280
1000Genomes	Europe	Sub	1006	AAACT=0.5586	delAAACT=0.4414
1000Genomes	South Asian	Sub	978	AAACT=0.539	delAAACT=0.461
1000Genomes	American	Sub	694	AAACT=0.448	delAAACT=0.552

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.29495056_29495060del
GRCh37.p13 chr 10	NC_000010.10:g.29783985_29783989del
SVIL RefSeqGene	NG_033998.1:g.245742_245746del

Gene: SVIL, supervillin (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SVIL transcript variant 3	NM_001323599.2:c.2824+32_… NM_001323599.2:c.2824+32_2824+36del	N/A	Intron Variant
SVIL transcript variant 4	NM_001323600.1:c.2572+32_… NM_001323600.1:c.2572+32_2572+36del	N/A	Intron Variant
SVIL transcript variant 1	NM_003174.3:c.2476+32_247… NM_003174.3:c.2476+32_2476+36del	N/A	Intron Variant
SVIL transcript variant 2	NM_021738.3:c.3754+32_375… NM_021738.3:c.3754+32_3754+36del	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.

Allele: delAAACT (allele ID: 1248887 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001669063.2	not provided	Benign

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	AAACT=	delAAACT
GRCh38.p14 chr 10	NC_000010.11:g.29495056_29495060=	NC_000010.11:g.29495056_29495060del
GRCh37.p13 chr 10	NC_000010.10:g.29783985_29783989=	NC_000010.10:g.29783985_29783989del
SVIL RefSeqGene	NG_033998.1:g.245742_245746=	NG_033998.1:g.245742_245746del
SVIL transcript variant 3	NM_001323599.2:c.2824+36=	NM_001323599.2:c.2824+32_2824+36del
SVIL transcript variant 4	NM_001323600.1:c.2572+36=	NM_001323600.1:c.2572+32_2572+36del
SVIL transcript variant 1	NM_003174.3:c.2476+36=	NM_003174.3:c.2476+32_2476+36del
SVIL transcript variant 2	NM_021738.2:c.3754+36=	NM_021738.2:c.3754+32_3754+36del
SVIL transcript variant 2	NM_021738.3:c.3754+36=	NM_021738.3:c.3754+32_3754+36del
SVIL transcript variant X1	XM_005252564.1:c.4114+36=	XM_005252564.1:c.4114+32_4114+36del
SVIL transcript variant X2	XM_005252565.1:c.4036+36=	XM_005252565.1:c.4036+32_4036+36del
SVIL transcript variant X3	XM_005252566.1:c.4018+36=	XM_005252566.1:c.4018+32_4018+36del
SVIL transcript variant X4	XM_005252567.1:c.3988+36=	XM_005252567.1:c.3988+32_3988+36del
SVIL transcript variant X5	XM_005252568.1:c.3943+36=	XM_005252568.1:c.3943+32_3943+36del
SVIL transcript variant X6	XM_005252569.1:c.3892+36=	XM_005252569.1:c.3892+32_3892+36del
SVIL transcript variant X7	XM_005252570.1:c.3880+36=	XM_005252570.1:c.3880+32_3880+36del
SVIL transcript variant X8	XM_005252571.1:c.3880+36=	XM_005252571.1:c.3880+32_3880+36del
SVIL transcript variant X9	XM_005252572.1:c.3880+36=	XM_005252572.1:c.3880+32_3880+36del
SVIL transcript variant X10	XM_005252573.1:c.3880+36=	XM_005252573.1:c.3880+32_3880+36del

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#.

54 SubSNP, 8 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4262546	Jan 05, 2002 (102)
2	DEVINE_LAB	ss14967657	Mar 15, 2016 (147)
3	HGSV	ss77862281	Dec 07, 2007 (129)
4	HGSV	ss77866054	Dec 07, 2007 (129)
5	HGSV	ss82246127	Dec 15, 2007 (130)
6	HGSV	ss83558710	Dec 15, 2007 (130)
7	HUMANGENOME_JCVI	ss95537227	Feb 06, 2009 (130)
8	BCMHGSC_JDW	ss103506816	Dec 01, 2009 (131)
9	GMI	ss155327096	Dec 01, 2009 (131)
10	BUSHMAN	ss193176536	Jul 04, 2010 (132)
11	GMI	ss289005331	May 04, 2012 (137)
12	PJP	ss294649704	May 09, 2011 (135)
13	1000GENOMES	ss327302791	May 09, 2011 (135)
14	1000GENOMES	ss499179900	May 04, 2012 (137)
15	LUNTER	ss552013354	Apr 25, 2013 (138)
16	LUNTER	ss552255967	Apr 25, 2013 (138)
17	LUNTER	ss553406096	Apr 25, 2013 (138)
18	1000GENOMES	ss1369308086	Aug 21, 2014 (142)
19	EVA_EXAC	ss1711934966	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1806327140	Sep 08, 2015 (146)
21	JJLAB	ss2031009828	Sep 14, 2016 (149)
22	SYSTEMSBIOZJU	ss2627504675	Nov 08, 2017 (151)
23	GNOMAD	ss2738181635	Nov 08, 2017 (151)
24	GNOMAD	ss2748367841	Nov 08, 2017 (151)
25	SWEGEN	ss3006179507	Nov 08, 2017 (151)
26	MCHAISSO	ss3063646794	Nov 08, 2017 (151)
27	MCHAISSO	ss3064466408	Nov 08, 2017 (151)
28	MCHAISSO	ss3065374900	Nov 08, 2017 (151)
29	BEROUKHIMLAB	ss3644296180	Oct 12, 2018 (152)
30	BIOINF_KMB_FNS_UNIBA	ss3645127484	Oct 12, 2018 (152)
31	URBANLAB	ss3649326414	Oct 12, 2018 (152)
32	EVA_DECODE	ss3689575660	Jul 13, 2019 (153)
33	PACBIO	ss3786626457	Jul 13, 2019 (153)
34	PACBIO	ss3791813238	Jul 13, 2019 (153)
35	PACBIO	ss3796695236	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3813291868	Jul 13, 2019 (153)
37	EVA	ss3824510203	Apr 26, 2020 (154)
38	EVA	ss3832048013	Apr 26, 2020 (154)
39	EVA	ss3986480335	Apr 26, 2021 (155)
40	TOMMO_GENOMICS	ss5196919242	Apr 26, 2021 (155)
41	EVA	ss5237208263	Apr 26, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5577065803	Oct 16, 2022 (156)
43	EVA	ss5623948946	Oct 16, 2022 (156)
44	EVA	ss5624007827	Oct 16, 2022 (156)
45	SANFORD_IMAGENETICS	ss5648973076	Oct 16, 2022 (156)
46	TOMMO_GENOMICS	ss5741961466	Oct 16, 2022 (156)
47	EVA	ss5800061542	Oct 16, 2022 (156)
48	EVA	ss5800158486	Oct 16, 2022 (156)
49	YY_MCH	ss5811331500	Oct 16, 2022 (156)
50	EVA	ss5824182503	Oct 16, 2022 (156)
51	EVA	ss5848296298	Oct 16, 2022 (156)
52	EVA	ss5849504761	Oct 16, 2022 (156)
53	EVA	ss5940266378	Oct 16, 2022 (156)
54	EVA	ss5980605083	Oct 16, 2022 (156)
55	1000Genomes	NC_000010.10 - 29783985	Oct 12, 2018 (152)
56	1000Genomes_30x	NC_000010.11 - 29495056	Oct 16, 2022 (156)
57	ExAC	NC_000010.10 - 29783985	Oct 12, 2018 (152)
58	gnomAD - Exomes	NC_000010.10 - 29783985	Jul 13, 2019 (153)
59	GO Exome Sequencing Project	NC_000010.10 - 29783985	Oct 12, 2018 (152)
60	8.3KJPN	NC_000010.10 - 29783985	Apr 26, 2021 (155)
61	14KJPN	NC_000010.11 - 29495056	Oct 16, 2022 (156)
62	ALFA	NC_000010.11 - 29495056	Apr 26, 2021 (155)
63	ClinVar	RCV001669063.2	Oct 16, 2022 (156)

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)
rs33916879	Oct 16, 2006 (127)
rs60312591	May 25, 2008 (130)
rs144145997	Sep 17, 2011 (135)
rs145157093	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77862281, ss77866054, ss82246127, ss83558710	NC_000010.8:29823990:AAACT:	NC_000010.11:29495055:AAACT:	(self)
ss289005331, ss294649704, ss327302791, ss552013354, ss552255967, ss553406096	NC_000010.9:29823990:AAACT:	NC_000010.11:29495055:AAACT:	(self)
49218845, 78784, 7378549, 967927, 54888549, ss499179900, ss1369308086, ss1711934966, ss1806327140, ss2031009828, ss2627504675, ss2738181635, ss2748367841, ss3006179507, ss3644296180, ss3786626457, ss3791813238, ss3796695236, ss3824510203, ss3832048013, ss3986480335, ss5196919242, ss5623948946, ss5624007827, ss5648973076, ss5800061542, ss5800158486, ss5824182503, ss5848296298, ss5940266378, ss5980605083	NC_000010.10:29783984:AAACT:	NC_000010.11:29495055:AAACT:	(self)
RCV001669063.2, 64591738, 75798570, 3650141761, ss3063646794, ss3064466408, ss3065374900, ss3645127484, ss3649326414, ss3689575660, ss3813291868, ss5237208263, ss5577065803, ss5741961466, ss5811331500, ss5849504761	NC_000010.11:29495055:AAACT:	NC_000010.11:29495055:AAACT:	(self)
ss4262546, ss14967657, ss95537227, ss103506816, ss155327096	NT_008705.16:29723984:AAACT:	NC_000010.11:29495055:AAACT:	(self)
ss193176536	NT_008705.17:29485055:AAACT:	NC_000010.11:29495055:AAACT:	(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 rs3031505

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

rs3031505