Name: rs79093943
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.

rs79093943

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:52553853 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.030779 (8147/264690, TOPMED)
C=0.038302 (5364/140044, GnomAD)
C=0.05326 (1006/18890, ALFA) (+ 13 more)
C=0.0222 (142/6404, 1000G_30x)
C=0.0222 (111/5008, 1000G)
C=0.0984 (441/4480, Estonian)
C=0.0540 (208/3854, ALSPAC)
C=0.0472 (175/3708, TWINSUK)
C=0.053 (53/998, GoNL)
C=0.072 (43/600, NorthernSweden)
C=0.019 (4/216, Qatari)
C=0.005 (1/216, Vietnamese)
C=0.07 (3/40, GENOME_DK)
G=0.50 (10/20, SGDP_PRJ)
C=0.50 (10/20, SGDP_PRJ)
G=0.2 (1/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DCC : 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=0.94674	C=0.05326
European	Sub	14286	G=0.93490	C=0.06510
African	Sub	2946	G=0.9885	C=0.0115
African Others	Sub	114	G=0.991	C=0.009
African American	Sub	2832	G=0.9883	C=0.0117
Asian	Sub	112	G=1.000	C=0.000
East Asian	Sub	86	G=1.00	C=0.00
Other Asian	Sub	26	G=1.00	C=0.00
Latin American 1	Sub	146	G=0.966	C=0.034
Latin American 2	Sub	610	G=0.989	C=0.011
South Asian	Sub	98	G=0.96	C=0.04
Other	Sub	692	G=0.962	C=0.038

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=0.969221	C=0.030779
gnomAD - Genomes	Global	Study-wide	140044	G=0.961698	C=0.038302
gnomAD - Genomes	European	Sub	75868	G=0.94282	C=0.05718
gnomAD - Genomes	African	Sub	41982	G=0.98657	C=0.01343
gnomAD - Genomes	American	Sub	13608	G=0.97994	C=0.02006
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	G=0.9662	C=0.0338
gnomAD - Genomes	East Asian	Sub	3124	G=0.9987	C=0.0013
gnomAD - Genomes	Other	Sub	2146	G=0.9660	C=0.0340
Allele Frequency Aggregator	Total	Global	18890	G=0.94674	C=0.05326
Allele Frequency Aggregator	European	Sub	14286	G=0.93490	C=0.06510
Allele Frequency Aggregator	African	Sub	2946	G=0.9885	C=0.0115
Allele Frequency Aggregator	Other	Sub	692	G=0.962	C=0.038
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.989	C=0.011
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.966	C=0.034
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.96	C=0.04
1000Genomes_30x	Global	Study-wide	6404	G=0.9778	C=0.0222
1000Genomes_30x	African	Sub	1786	G=0.9894	C=0.0106
1000Genomes_30x	Europe	Sub	1266	G=0.9573	C=0.0427
1000Genomes_30x	South Asian	Sub	1202	G=0.9651	C=0.0349
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	G=0.972	C=0.028
1000Genomes	Global	Study-wide	5008	G=0.9778	C=0.0222
1000Genomes	African	Sub	1322	G=0.9894	C=0.0106
1000Genomes	East Asian	Sub	1008	G=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	G=0.9533	C=0.0467
1000Genomes	South Asian	Sub	978	G=0.967	C=0.033
1000Genomes	American	Sub	694	G=0.974	C=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9016	C=0.0984
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9460	C=0.0540
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9528	C=0.0472
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.947	C=0.053
Northern Sweden	ACPOP	Study-wide	600	G=0.928	C=0.072
Qatari	Global	Study-wide	216	G=0.981	C=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.995	C=0.005
The Danish reference pan genome	Danish	Study-wide	40	G=0.93	C=0.07
SGDP_PRJ	Global	Study-wide	20	G=0.50	C=0.50
Siberian	Global	Study-wide	4	G=0.2	C=0.8

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 18	NC_000018.10:g.52553853G>C
GRCh37.p13 chr 18	NC_000018.9:g.50080223G>C
DCC RefSeqGene (LRG_1107)	NG_013341.2:g.218682G>C

Gene: DCC, DCC netrin 1 receptor (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DCC transcript	NM_005215.4:c.92-198201G>C	N/A	Intron Variant
DCC transcript variant X1	XM_017025568.2:c.92-19820… XM_017025568.2:c.92-198201G>C	N/A	Intron Variant
DCC transcript variant X2	XM_017025569.2:c.92-19820… XM_017025569.2:c.92-198201G>C	N/A	Intron Variant
DCC transcript variant X3	XM_047437311.1:c.92-19820… XM_047437311.1:c.92-198201G>C	N/A	Intron Variant
DCC transcript variant X4	XM_011525844.3:c.	N/A	Genic Upstream 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	G=	C
GRCh38.p14 chr 18	NC_000018.10:g.52553853=	NC_000018.10:g.52553853G>C
GRCh37.p13 chr 18	NC_000018.9:g.50080223=	NC_000018.9:g.50080223G>C
DCC RefSeqGene (LRG_1107)	NG_013341.2:g.218682=	NG_013341.2:g.218682G>C
DCC transcript	NM_005215.3:c.92-198201=	NM_005215.3:c.92-198201G>C
DCC transcript	NM_005215.4:c.92-198201=	NM_005215.4:c.92-198201G>C
DCC transcript variant X1	XM_005258204.1:c.92-198201=	XM_005258204.1:c.92-198201G>C
DCC transcript variant X1	XM_017025568.2:c.92-198201=	XM_017025568.2:c.92-198201G>C
DCC transcript variant X2	XM_017025569.2:c.92-198201=	XM_017025569.2:c.92-198201G>C
DCC transcript variant X3	XM_047437311.1:c.92-198201=	XM_047437311.1:c.92-198201G>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#.

31 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss237478510	Jul 15, 2010 (132)
2	EVA-GONL	ss993762510	Aug 21, 2014 (142)
3	JMKIDD_LAB	ss1081525246	Aug 21, 2014 (142)
4	1000GENOMES	ss1361164089	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1578417239	Apr 01, 2015 (144)
6	EVA_UK10K_ALSPAC	ss1636950131	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1679944164	Apr 01, 2015 (144)
8	EVA_DECODE	ss1697822879	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1937230144	Feb 12, 2016 (147)
10	JJLAB	ss2029384679	Sep 14, 2016 (149)
11	USC_VALOUEV	ss2157891197	Dec 20, 2016 (150)
12	HUMAN_LONGEVITY	ss2221860703	Dec 20, 2016 (150)
13	GNOMAD	ss2957077650	Nov 08, 2017 (151)
14	SWEGEN	ss3016581781	Nov 08, 2017 (151)
15	BIOINF_KMB_FNS_UNIBA	ss3028521223	Nov 08, 2017 (151)
16	CSHL	ss3352038139	Nov 08, 2017 (151)
17	EGCUT_WGS	ss3683425275	Jul 13, 2019 (153)
18	EVA_DECODE	ss3701726273	Jul 13, 2019 (153)
19	ACPOP	ss3742571931	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3820690458	Jul 13, 2019 (153)
21	EVA	ss3835185863	Apr 27, 2020 (154)
22	SGDP_PRJ	ss3887089608	Apr 27, 2020 (154)
23	TOPMED	ss5057927540	Apr 26, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5305412554	Oct 16, 2022 (156)
25	EVA	ss5431644362	Oct 16, 2022 (156)
26	HUGCELL_USP	ss5498170373	Oct 16, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5610318087	Oct 16, 2022 (156)
28	SANFORD_IMAGENETICS	ss5661362243	Oct 16, 2022 (156)
29	EVA	ss5827590962	Oct 16, 2022 (156)
30	EVA	ss5874222967	Oct 16, 2022 (156)
31	EVA	ss5952782512	Oct 16, 2022 (156)
32	1000Genomes	NC_000018.9 - 50080223	Oct 12, 2018 (152)
33	1000Genomes_30x	NC_000018.10 - 52553853	Oct 16, 2022 (156)
34	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 50080223	Oct 12, 2018 (152)
35	Genetic variation in the Estonian population	NC_000018.9 - 50080223	Oct 12, 2018 (152)
36	The Danish reference pan genome	NC_000018.9 - 50080223	Apr 27, 2020 (154)
37	gnomAD - Genomes	NC_000018.10 - 52553853	Apr 26, 2021 (155)
38	Genome of the Netherlands Release 5	NC_000018.9 - 50080223	Apr 27, 2020 (154)
39	Northern Sweden	NC_000018.9 - 50080223	Jul 13, 2019 (153)
40	Qatari	NC_000018.9 - 50080223	Apr 27, 2020 (154)
41	SGDP_PRJ	NC_000018.9 - 50080223	Apr 27, 2020 (154)
42	Siberian	NC_000018.9 - 50080223	Apr 27, 2020 (154)
43	TopMed	NC_000018.10 - 52553853	Apr 26, 2021 (155)
44	UK 10K study - Twins	NC_000018.9 - 50080223	Oct 12, 2018 (152)
45	A Vietnamese Genetic Variation Database	NC_000018.9 - 50080223	Jul 13, 2019 (153)
46	ALFA	NC_000018.10 - 52553853	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
ss1697822879	NC_000018.8:48334220:G:C	NC_000018.10:52553852:G:C	(self)
74497725, 41280340, 29163523, 4608727, 18389424, 15856796, 19272066, 39106588, 10407551, 41280340, 9120499, ss237478510, ss993762510, ss1081525246, ss1361164089, ss1578417239, ss1636950131, ss1679944164, ss1937230144, ss2029384679, ss2157891197, ss2957077650, ss3016581781, ss3352038139, ss3683425275, ss3742571931, ss3835185863, ss3887089608, ss5431644362, ss5661362243, ss5827590962, ss5952782512	NC_000018.9:50080222:G:C	NC_000018.10:52553852:G:C	(self)
97844022, 525536192, 273473203, 9659862667, ss2221860703, ss3028521223, ss3701726273, ss3820690458, ss5057927540, ss5305412554, ss5498170373, ss5610318087, ss5874222967	NC_000018.10:52553852:G:C	NC_000018.10:52553852: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 rs79093943

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

rs79093943