Name: rs185692842
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.

rs185692842

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:53795678 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.00004 (1/28258, 14KJPN)
G=0.00191 (36/18812, ALFA)
G=0.00006 (1/16760, 8.3KJPN) (+ 9 more)
G=0.0014 (9/6404, 1000G_30x)
G=0.0014 (7/5008, 1000G)
G=0.0056 (25/4480, Estonian)
G=0.0034 (13/3854, ALSPAC)
G=0.0057 (21/3708, TWINSUK)
G=0.0003 (1/2922, KOREAN)
G=0.0000 (0/1832, Korea1K)
G=0.008 (8/998, GoNL)
G=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NDC1 : 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	18812	C=0.99809	G=0.00191, T=0.00000
European	Sub	14214	C=0.99747	G=0.00253, T=0.00000
African	Sub	2944	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	2830	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	112	C=1.000	G=0.000, T=0.000
East Asian	Sub	86	C=1.00	G=0.00, T=0.00
Other Asian	Sub	26	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	606	C=1.000	G=0.000, T=0.000
South Asian	Sub	98	C=1.00	G=0.00, T=0.00
Other	Sub	692	C=1.000	G=0.000, T=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
14KJPN	JAPANESE	Study-wide	28258	C=0.99996	G=0.00004
Allele Frequency Aggregator	Total	Global	18812	C=0.99809	G=0.00191, T=0.00000
Allele Frequency Aggregator	European	Sub	14214	C=0.99747	G=0.00253, T=0.00000
Allele Frequency Aggregator	African	Sub	2944	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	692	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	606	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	G=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99994	G=0.00006
1000Genomes_30x	Global	Study-wide	6404	C=0.9986	G=0.0014
1000Genomes_30x	African	Sub	1786	C=1.0000	G=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9945	G=0.0055
1000Genomes_30x	South Asian	Sub	1202	C=0.9983	G=0.0017
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	G=0.0000
1000Genomes_30x	American	Sub	980	C=1.000	G=0.000
1000Genomes	Global	Study-wide	5008	C=0.9986	G=0.0014
1000Genomes	African	Sub	1322	C=1.0000	G=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	G=0.0000
1000Genomes	Europe	Sub	1006	C=0.9940	G=0.0060
1000Genomes	South Asian	Sub	978	C=0.999	G=0.001
1000Genomes	American	Sub	694	C=1.000	G=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9944	G=0.0056
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9966	G=0.0034
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9943	G=0.0057
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9997	G=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	C=1.0000	G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.992	G=0.008
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	G=0.03

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 1	NC_000001.11:g.53795678C>G
GRCh38.p14 chr 1	NC_000001.11:g.53795678C>T
GRCh37.p13 chr 1	NC_000001.10:g.54261351C>G
GRCh37.p13 chr 1	NC_000001.10:g.54261351C>T

Gene: NDC1, NDC1 transmembrane nucleoporin (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NDC1 transcript variant 2	NM_001168551.2:c.1464+101… NM_001168551.2:c.1464+1011G>C	N/A	Intron Variant
NDC1 transcript variant 1	NM_018087.5:c.1584+1011G>C	N/A	Intron Variant
NDC1 transcript variant 3	NR_033142.2:n.	N/A	Intron Variant
NDC1 transcript variant X1	XM_011541766.3:c.1581+101… XM_011541766.3:c.1581+1011G>C	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.

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	C=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.53795678=	NC_000001.11:g.53795678C>G	NC_000001.11:g.53795678C>T
GRCh37.p13 chr 1	NC_000001.10:g.54261351=	NC_000001.10:g.54261351C>G	NC_000001.10:g.54261351C>T
NDC1 transcript variant 2	NM_001168551.1:c.1464+1011=	NM_001168551.1:c.1464+1011G>C	NM_001168551.1:c.1464+1011G>A
NDC1 transcript variant 2	NM_001168551.2:c.1464+1011=	NM_001168551.2:c.1464+1011G>C	NM_001168551.2:c.1464+1011G>A
NDC1 transcript variant 1	NM_018087.4:c.1584+1011=	NM_018087.4:c.1584+1011G>C	NM_018087.4:c.1584+1011G>A
NDC1 transcript variant 1	NM_018087.5:c.1584+1011=	NM_018087.5:c.1584+1011G>C	NM_018087.5:c.1584+1011G>A
NDC1 transcript variant X1	XM_011541766.3:c.1581+1011=	XM_011541766.3:c.1581+1011G>C	XM_011541766.3:c.1581+1011G>A

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#.

25 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss454059459	Sep 17, 2011 (135)
2	EVA-GONL	ss975151084	Aug 21, 2014 (142)
3	1000GENOMES	ss1290858353	Aug 21, 2014 (142)
4	EVA_GENOME_DK	ss1574052685	Apr 01, 2015 (144)
5	EVA_DECODE	ss1584517112	Apr 01, 2015 (144)
6	EVA_UK10K_ALSPAC	ss1600155198	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1643149231	Apr 01, 2015 (144)
8	HUMAN_LONGEVITY	ss2162434878	Dec 20, 2016 (150)
9	GNOMAD	ss2755057648	Nov 08, 2017 (151)
10	SWEGEN	ss2986803188	Nov 08, 2017 (151)
11	EGCUT_WGS	ss3654866724	Jul 12, 2019 (153)
12	EVA_DECODE	ss3686754040	Jul 12, 2019 (153)
13	KRGDB	ss3893836101	Apr 25, 2020 (154)
14	KOGIC	ss3944493400	Apr 25, 2020 (154)
15	TOPMED	ss4449457113	Apr 25, 2021 (155)
16	TOPMED	ss4449457114	Apr 25, 2021 (155)
17	TOMMO_GENOMICS	ss5143911808	Apr 25, 2021 (155)
18	1000G_HIGH_COVERAGE	ss5242239418	Oct 12, 2022 (156)
19	EVA	ss5318669607	Oct 12, 2022 (156)
20	HUGCELL_USP	ss5443303788	Oct 12, 2022 (156)
21	1000G_HIGH_COVERAGE	ss5514501767	Oct 12, 2022 (156)
22	TOMMO_GENOMICS	ss5668673550	Oct 12, 2022 (156)
23	EVA	ss5831947077	Oct 12, 2022 (156)
24	EVA	ss5908224723	Oct 12, 2022 (156)
25	EVA	ss5937342593	Oct 12, 2022 (156)
26	1000Genomes	NC_000001.10 - 54261351	Oct 11, 2018 (152)
27	1000Genomes_30x	NC_000001.11 - 53795678	Oct 12, 2022 (156)
28	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 54261351	Oct 11, 2018 (152)
29	Genetic variation in the Estonian population	NC_000001.10 - 54261351	Oct 11, 2018 (152)
30	The Danish reference pan genome	NC_000001.10 - 54261351	Apr 25, 2020 (154)
31	gnomAD - Genomes Submission ignored due to conflicting rows: Row 11161492 (NC_000001.11:53795677:C:G 524/140228) Row 11161493 (NC_000001.11:53795677:C:T 1/140228)	-	Apr 25, 2021 (155)
32	gnomAD - Genomes Submission ignored due to conflicting rows: Row 11161492 (NC_000001.11:53795677:C:G 524/140228) Row 11161493 (NC_000001.11:53795677:C:T 1/140228)	-	Apr 25, 2021 (155)
33	Genome of the Netherlands Release 5	NC_000001.10 - 54261351	Apr 25, 2020 (154)
34	KOREAN population from KRGDB	NC_000001.10 - 54261351	Apr 25, 2020 (154)
35	Korean Genome Project	NC_000001.11 - 53795678	Apr 25, 2020 (154)
36	8.3KJPN	NC_000001.10 - 54261351	Apr 25, 2021 (155)
37	14KJPN	NC_000001.11 - 53795678	Oct 12, 2022 (156)
38	TopMed Submission ignored due to conflicting rows: Row 13063448 (NC_000001.11:53795677:C:G 712/264690) Row 13063449 (NC_000001.11:53795677:C:T 3/264690)	-	Apr 25, 2021 (155)
39	TopMed Submission ignored due to conflicting rows: Row 13063448 (NC_000001.11:53795677:C:G 712/264690) Row 13063449 (NC_000001.11:53795677:C:T 3/264690)	-	Apr 25, 2021 (155)
40	UK 10K study - Twins	NC_000001.10 - 54261351	Oct 11, 2018 (152)
41	ALFA	NC_000001.11 - 53795678	Apr 25, 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
ss1584517112	NC_000001.9:54033938:C:G	NC_000001.11:53795677:C:G	(self)
1575479, 856297, 604972, 1497852, 362829, 1013495, 1881115, 856297, ss454059459, ss975151084, ss1290858353, ss1574052685, ss1600155198, ss1643149231, ss2755057648, ss2986803188, ss3654866724, ss3893836101, ss5143911808, ss5318669607, ss5831947077, ss5937342593	NC_000001.10:54261350:C:G	NC_000001.11:53795677:C:G	(self)
2027702, 871401, 2510654, 12544307030, ss2162434878, ss3686754040, ss3944493400, ss4449457113, ss5242239418, ss5443303788, ss5514501767, ss5668673550, ss5908224723	NC_000001.11:53795677:C:G	NC_000001.11:53795677:C:G	(self)
12544307030, ss4449457114	NC_000001.11:53795677:C:T	NC_000001.11:53795677:C:T	(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 rs185692842

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

rs185692842