Name: rs1489634913
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.

rs1489634913

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:185427685 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.022333 (2963/132676, GnomAD)
G=0.00103 (29/28258, 14KJPN)
G=0.00095 (16/16760, 8.3KJPN) (+ 7 more)
G=0.03998 (667/16684, ALFA)
G=0.0309 (198/6404, 1000G_30x)
G=0.0603 (269/4464, Estonian)
G=0.0017 (5/2922, KOREAN)
G=0.098 (59/600, NorthernSweden)
A=0.50 (14/28, SGDP_PRJ)
G=0.50 (14/28, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C4orf47 : Intron Variant
UFSP2 : 2KB Upstream 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	16684	A=0.96002	G=0.03998	0.92316	0.003117	0.073723	8
European	Sub	12196	A=0.95335	G=0.04665	0.910298	0.003608	0.086094	4
African	Sub	2864	A=0.9815	G=0.0185	0.965782	0.002793	0.031425	14
African Others	Sub	108	A=1.000	G=0.000	1.0	0.0	0.0	N/A
African American	Sub	2756	A=0.9808	G=0.0192	0.964441	0.002903	0.032656	14
Asian	Sub	108	A=1.000	G=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	A=1.00	G=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	A=1.00	G=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	A=0.979	G=0.021	0.958904	0.0	0.041096	0
Latin American 2	Sub	610	A=0.964	G=0.036	0.927869	0.0	0.072131	0
South Asian	Sub	94	A=0.96	G=0.04	0.914894	0.0	0.085106	0
Other	Sub	666	A=0.976	G=0.024	0.951952	0.0	0.048048	0

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 - Genomes	Global	Study-wide	132676	A=0.977667	G=0.022333
gnomAD - Genomes	European	Sub	70820	A=0.96999	G=0.03001
gnomAD - Genomes	African	Sub	40654	A=0.98805	G=0.01195
gnomAD - Genomes	American	Sub	12824	A=0.97778	G=0.02222
gnomAD - Genomes	Ashkenazi Jewish	Sub	3240	A=0.9917	G=0.0083
gnomAD - Genomes	East Asian	Sub	3126	A=0.9997	G=0.0003
gnomAD - Genomes	Other	Sub	2012	A=0.9806	G=0.0194
14KJPN	JAPANESE	Study-wide	28258	A=0.99897	G=0.00103
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99905	G=0.00095
Allele Frequency Aggregator	Total	Global	16684	A=0.96002	G=0.03998
Allele Frequency Aggregator	European	Sub	12196	A=0.95335	G=0.04665
Allele Frequency Aggregator	African	Sub	2864	A=0.9815	G=0.0185
Allele Frequency Aggregator	Other	Sub	666	A=0.976	G=0.024
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.964	G=0.036
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.979	G=0.021
Allele Frequency Aggregator	Asian	Sub	108	A=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	94	A=0.96	G=0.04
1000Genomes_30x	Global	Study-wide	6404	A=0.9691	G=0.0309
1000Genomes_30x	African	Sub	1786	A=0.9838	G=0.0162
1000Genomes_30x	Europe	Sub	1266	A=0.9637	G=0.0363
1000Genomes_30x	South Asian	Sub	1202	A=0.9376	G=0.0624
1000Genomes_30x	East Asian	Sub	1170	A=0.9974	G=0.0026
1000Genomes_30x	American	Sub	980	A=0.954	G=0.046
Genetic variation in the Estonian population	Estonian	Study-wide	4464	A=0.9397	G=0.0603
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9983	G=0.0017
Northern Sweden	ACPOP	Study-wide	600	A=0.902	G=0.098
SGDP_PRJ	Global	Study-wide	28	A=0.50	G=0.50

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 4	NC_000004.12:g.185427685A>G
GRCh37.p13 chr 4	NC_000004.11:g.186348839A>G
UFSP2 RefSeqGene	NG_051609.1:g.3301T>C

Gene: C4orf47, chromosome 4 open reading frame 47 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CFAP96 transcript variant 1	NM_001114357.3:c.-79+1289… NM_001114357.3:c.-79+1289A>G	N/A	Intron Variant
CFAP96 transcript variant 2	NM_001346007.2:c.-161+128… NM_001346007.2:c.-161+1289A>G	N/A	Intron Variant
CFAP96 transcript variant X1	XM_011531989.3:c.-79+439A… XM_011531989.3:c.-79+439A>G	N/A	Intron Variant
CFAP96 transcript variant X5	XM_017008238.2:c.-78-1649… XM_017008238.2:c.-78-1649A>G	N/A	Intron Variant
CFAP96 transcript variant X6	XM_017008239.2:c.-81-1646… XM_017008239.2:c.-81-1646A>G	N/A	Intron Variant
CFAP96 transcript variant X4	XM_017008240.2:c.-82+439A… XM_017008240.2:c.-82+439A>G	N/A	Intron Variant
CFAP96 transcript variant X2	XM_047415718.1:c.-82+1289… XM_047415718.1:c.-82+1289A>G	N/A	Intron Variant
CFAP96 transcript variant X3	XM_047415719.1:c.-79+1264… XM_047415719.1:c.-79+1264A>G	N/A	Intron Variant
CFAP96 transcript variant X7	XM_047415720.1:c.-164+128… XM_047415720.1:c.-164+1289A>G	N/A	Intron Variant
CFAP96 transcript variant X8	XM_047415721.1:c.-161+439… XM_047415721.1:c.-161+439A>G	N/A	Intron Variant
CFAP96 transcript variant X9	XM_047415722.1:c.-82+439A… XM_047415722.1:c.-82+439A>G	N/A	Intron Variant

Gene: UFSP2, UFM1 specific peptidase 2 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
UFSP2 transcript variant 1	NM_018359.5:c.	N/A	Upstream Transcript Variant
UFSP2 transcript variant 2	NR_028085.2:n.	N/A	Upstream Transcript Variant
UFSP2 transcript variant 3	NR_144317.2:n.	N/A	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	A=	G
GRCh38.p14 chr 4	NC_000004.12:g.185427685=	NC_000004.12:g.185427685A>G
GRCh37.p13 chr 4	NC_000004.11:g.186348839=	NC_000004.11:g.186348839A>G
UFSP2 RefSeqGene	NG_051609.1:g.3301=	NG_051609.1:g.3301T>C
CFAP96 transcript variant 1	NM_001114357.3:c.-79+1289=	NM_001114357.3:c.-79+1289A>G
CFAP96 transcript variant 2	NM_001346007.2:c.-161+1289=	NM_001346007.2:c.-161+1289A>G
C4orf47 transcript variant X1	XM_005263018.1:c.-79+1289=	XM_005263018.1:c.-79+1289A>G
C4orf47 transcript variant X2	XM_005263019.1:c.-79+1289=	XM_005263019.1:c.-79+1289A>G
C4orf47 transcript variant X3	XM_005263020.1:c.-82+1289=	XM_005263020.1:c.-82+1289A>G
C4orf47 transcript variant X4	XM_005263021.1:c.-161+1289=	XM_005263021.1:c.-161+1289A>G
CFAP96 transcript variant X1	XM_011531989.3:c.-79+439=	XM_011531989.3:c.-79+439A>G
CFAP96 transcript variant X5	XM_017008238.2:c.-78-1649=	XM_017008238.2:c.-78-1649A>G
CFAP96 transcript variant X6	XM_017008239.2:c.-81-1646=	XM_017008239.2:c.-81-1646A>G
CFAP96 transcript variant X4	XM_017008240.2:c.-82+439=	XM_017008240.2:c.-82+439A>G
CFAP96 transcript variant X2	XM_047415718.1:c.-82+1289=	XM_047415718.1:c.-82+1289A>G
CFAP96 transcript variant X3	XM_047415719.1:c.-79+1264=	XM_047415719.1:c.-79+1264A>G
CFAP96 transcript variant X7	XM_047415720.1:c.-164+1289=	XM_047415720.1:c.-164+1289A>G
CFAP96 transcript variant X8	XM_047415721.1:c.-161+439=	XM_047415721.1:c.-161+439A>G
CFAP96 transcript variant X9	XM_047415722.1:c.-82+439=	XM_047415722.1:c.-82+439A>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#.

14 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2819763493	Nov 08, 2017 (151)
2	SWEGEN	ss2996207790	Nov 08, 2017 (151)
3	CSHL	ss3346159679	Nov 08, 2017 (151)
4	EGCUT_WGS	ss3664128798	Jul 13, 2019 (153)
5	ACPOP	ss3731968142	Jul 13, 2019 (153)
6	SGDP_PRJ	ss3860904849	Apr 26, 2020 (154)
7	KRGDB	ss3907291380	Apr 26, 2020 (154)
8	TOMMO_GENOMICS	ss5169794199	Apr 27, 2021 (155)
9	1000G_HIGH_COVERAGE	ss5262425166	Oct 17, 2022 (156)
10	EVA	ss5354838204	Oct 17, 2022 (156)
11	1000G_HIGH_COVERAGE	ss5545263904	Oct 17, 2022 (156)
12	SANFORD_IMAGENETICS	ss5636915849	Oct 17, 2022 (156)
13	TOMMO_GENOMICS	ss5705277822	Oct 17, 2022 (156)
14	EVA	ss5867097043	Oct 17, 2022 (156)
15	1000Genomes_30x	NC_000004.12 - 185427685	Oct 17, 2022 (156)
16	Genetic variation in the Estonian population	NC_000004.11 - 186348839	Oct 12, 2018 (152)
17	gnomAD - Genomes	NC_000004.12 - 185427685	Apr 27, 2021 (155)
18	KOREAN population from KRGDB	NC_000004.11 - 186348839	Apr 26, 2020 (154)
19	Northern Sweden	NC_000004.11 - 186348839	Jul 13, 2019 (153)
20	SGDP_PRJ	NC_000004.11 - 186348839	Apr 26, 2020 (154)
21	8.3KJPN	NC_000004.11 - 186348839	Apr 27, 2021 (155)
22	14KJPN	NC_000004.12 - 185427685	Oct 17, 2022 (156)
23	ALFA	NC_000004.12 - 185427685	Apr 27, 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
9867046, 14468774, 5253007, 12921829, 27763506, ss2819763493, ss2996207790, ss3346159679, ss3664128798, ss3731968142, ss3860904849, ss3907291380, ss5169794199, ss5354838204, ss5636915849	NC_000004.11:186348838:A:G	NC_000004.12:185427684:A:G	(self)
32789839, 176472108, 39114926, 5207957168, ss5262425166, ss5545263904, ss5705277822, ss5867097043	NC_000004.12:185427684:A:G	NC_000004.12:185427684:A: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 rs1489634913

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

rs1489634913