Name: rs146487477
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.

rs146487477

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:2253082 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.002210 (585/264690, TOPMED)
A=0.002310 (324/140264, GnomAD)
A=0.00275 (52/18890, ALFA) (+ 8 more)
A=0.0008 (5/6404, 1000G_30x)
A=0.0010 (5/5008, 1000G)
A=0.0011 (5/4480, Estonian)
A=0.0021 (8/3854, ALSPAC)
A=0.0030 (11/3708, TWINSUK)
A=0.004 (4/998, GoNL)
A=0.012 (7/600, NorthernSweden)
A=0.002 (1/534, MGP)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ECI1 : 2KB Upstream Variant
RNPS1 : 500B Downstream Variant
LOC107984839 : Non Coding Transcript 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=0.99725	A=0.00275
European	Sub	14286	G=0.99685	A=0.00315
African	Sub	2946	G=0.9990	A=0.0010
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2832	G=0.9989	A=0.0011
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=0.997	A=0.003
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	692	G=0.997	A=0.003

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.997790	A=0.002210
gnomAD - Genomes	Global	Study-wide	140264	G=0.997690	A=0.002310
gnomAD - Genomes	European	Sub	75948	G=0.99641	A=0.00359
gnomAD - Genomes	African	Sub	42050	G=0.99914	A=0.00086
gnomAD - Genomes	American	Sub	13654	G=0.99934	A=0.00066
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2154	G=0.9972	A=0.0028
Allele Frequency Aggregator	Total	Global	18890	G=0.99725	A=0.00275
Allele Frequency Aggregator	European	Sub	14286	G=0.99685	A=0.00315
Allele Frequency Aggregator	African	Sub	2946	G=0.9990	A=0.0010
Allele Frequency Aggregator	Other	Sub	692	G=0.997	A=0.003
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.997	A=0.003
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9992	A=0.0008
1000Genomes_30x	African	Sub	1786	G=0.9994	A=0.0006
1000Genomes_30x	Europe	Sub	1266	G=0.9976	A=0.0024
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.999	A=0.001
1000Genomes	Global	Study-wide	5008	G=0.9990	A=0.0010
1000Genomes	African	Sub	1322	G=0.9992	A=0.0008
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9970	A=0.0030
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.999	A=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9989	A=0.0011
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9979	A=0.0021
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9970	A=0.0030
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.996	A=0.004
Northern Sweden	ACPOP	Study-wide	600	G=0.988	A=0.012
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.998	A=0.002

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 16	NC_000016.10:g.2253082G>A
GRCh37.p13 chr 16	NC_000016.9:g.2303083G>A
ECI1 RefSeqGene	NG_047046.1:g.3520C>T

Gene: ECI1, enoyl-CoA delta isomerase 1 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ECI1 transcript variant 2	NM_001178029.2:c.	N/A	Upstream Transcript Variant
ECI1 transcript variant 1	NM_001919.4:c.	N/A	Upstream Transcript Variant

Gene: RNPS1, RNA binding protein with serine rich domain 1 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RNPS1 transcript variant 3	NM_001286625.1:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant 4	NM_001286626.2:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant 5	NM_001286627.2:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant 1	NM_006711.5:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant 2	NM_080594.4:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant 6	NR_104485.2:n.	N/A	Downstream Transcript Variant
RNPS1 transcript variant X1	XM_005255048.3:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant X2	XM_005255049.5:c.	N/A	Downstream Transcript Variant
RNPS1 transcript variant X3	XM_047433516.1:c.	N/A	Downstream Transcript Variant

Gene: LOC107984839, uncharacterized LOC107984839 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984839 transcript	XR_001752052.2:n.425G>A	N/A	Non Coding 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=	A
GRCh38.p14 chr 16	NC_000016.10:g.2253082=	NC_000016.10:g.2253082G>A
GRCh37.p13 chr 16	NC_000016.9:g.2303083=	NC_000016.9:g.2303083G>A
ECI1 RefSeqGene	NG_047046.1:g.3520=	NG_047046.1:g.3520C>T
LOC107984839 transcript	XR_001752052.2:n.425=	XR_001752052.2:n.425G>A
LOC107984839 transcript	XR_001752052.1:n.497=	XR_001752052.1:n.497G>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#.

21 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss339047110	May 09, 2011 (134)
2	EVA-GONL	ss992195781	Aug 21, 2014 (142)
3	1000GENOMES	ss1355043207	Aug 21, 2014 (142)
4	EVA_UK10K_ALSPAC	ss1633830781	Apr 01, 2015 (144)
5	EVA_UK10K_TWINSUK	ss1676824814	Apr 01, 2015 (144)
6	EVA_DECODE	ss1696227930	Apr 01, 2015 (144)
7	EVA_MGP	ss1711415407	Apr 01, 2015 (144)
8	HUMAN_LONGEVITY	ss2209946950	Dec 20, 2016 (150)
9	GNOMAD	ss2939386223	Nov 08, 2017 (151)
10	SWEGEN	ss3013931551	Nov 08, 2017 (151)
11	EGCUT_WGS	ss3681056978	Jul 13, 2019 (153)
12	EVA_DECODE	ss3698676016	Jul 13, 2019 (153)
13	ACPOP	ss3741265386	Jul 13, 2019 (153)
14	TOPMED	ss5004965331	Apr 27, 2021 (155)
15	1000G_HIGH_COVERAGE	ss5299838498	Oct 16, 2022 (156)
16	EVA	ss5421782070	Oct 16, 2022 (156)
17	1000G_HIGH_COVERAGE	ss5601924823	Oct 16, 2022 (156)
18	SANFORD_IMAGENETICS	ss5658297879	Oct 16, 2022 (156)
19	EVA	ss5845989734	Oct 16, 2022 (156)
20	EVA	ss5897949563	Oct 16, 2022 (156)
21	EVA	ss5949722405	Oct 16, 2022 (156)
22	1000Genomes	NC_000016.9 - 2303083	Oct 12, 2018 (152)
23	1000Genomes_30x	NC_000016.10 - 2253082	Oct 16, 2022 (156)
24	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 2303083	Oct 12, 2018 (152)
25	Genetic variation in the Estonian population	NC_000016.9 - 2303083	Oct 12, 2018 (152)
26	gnomAD - Genomes	NC_000016.10 - 2253082	Apr 27, 2021 (155)
27	Genome of the Netherlands Release 5	NC_000016.9 - 2303083	Apr 27, 2020 (154)
28	Medical Genome Project healthy controls from Spanish population	NC_000016.9 - 2303083	Apr 27, 2020 (154)
29	Northern Sweden	NC_000016.9 - 2303083	Jul 13, 2019 (153)
30	TopMed	NC_000016.10 - 2253082	Apr 27, 2021 (155)
31	UK 10K study - Twins	NC_000016.9 - 2303083	Oct 12, 2018 (152)
32	ALFA	NC_000016.10 - 2253082	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
ss1696227930	NC_000016.8:2243083:G:A	NC_000016.10:2253081:G:A	(self)
68170258, 37851414, 26795226, 16887701, 531167, 14550251, 37851414, ss339047110, ss992195781, ss1355043207, ss1633830781, ss1676824814, ss1711415407, ss2939386223, ss3013931551, ss3681056978, ss3741265386, ss5421782070, ss5658297879, ss5845989734, ss5949722405	NC_000016.9:2303082:G:A	NC_000016.10:2253081:G:A	(self)
89450758, 480457932, 220510992, 7889620765, ss2209946950, ss3698676016, ss5004965331, ss5299838498, ss5601924823, ss5897949563	NC_000016.10:2253081:G:A	NC_000016.10:2253081:G:A	(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 rs146487477

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs146487477