Name: rs62345101
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.

rs62345101

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:145126363 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.022679 (6003/264690, TOPMED)
T=0.022907 (3210/140132, GnomAD)
T=0.02684 (507/18890, ALFA) (+ 11 more)
T=0.0112 (72/6404, 1000G_30x)
T=0.0106 (53/5008, 1000G)
T=0.0199 (89/4480, Estonian)
T=0.0485 (187/3854, ALSPAC)
T=0.0375 (139/3708, TWINSUK)
T=0.0005 (1/1832, Korea1K)
T=0.043 (43/998, GoNL)
T=0.047 (28/600, NorthernSweden)
T=0.005 (1/216, Qatari)
T=0.05 (2/40, GENOME_DK)
C=0.4 (3/8, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCE1 : 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	C=0.97316	T=0.02684
European	Sub	14286	C=0.96766	T=0.03234
African	Sub	2946	C=0.9949	T=0.0051
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2832	C=0.9947	T=0.0053
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.993	T=0.007
Latin American 2	Sub	610	C=0.980	T=0.020
South Asian	Sub	98	C=0.97	T=0.03
Other	Sub	692	C=0.980	T=0.020

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	C=0.977321	T=0.022679
gnomAD - Genomes	Global	Study-wide	140132	C=0.977093	T=0.022907
gnomAD - Genomes	European	Sub	75900	C=0.96614	T=0.03386
gnomAD - Genomes	African	Sub	41980	C=0.99326	T=0.00674
gnomAD - Genomes	American	Sub	13654	C=0.98308	T=0.01692
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.9750	T=0.0250
gnomAD - Genomes	East Asian	Sub	3132	C=0.9994	T=0.0006
gnomAD - Genomes	Other	Sub	2150	C=0.9809	T=0.0191
Allele Frequency Aggregator	Total	Global	18890	C=0.97316	T=0.02684
Allele Frequency Aggregator	European	Sub	14286	C=0.96766	T=0.03234
Allele Frequency Aggregator	African	Sub	2946	C=0.9949	T=0.0051
Allele Frequency Aggregator	Other	Sub	692	C=0.980	T=0.020
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.980	T=0.020
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.993	T=0.007
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.97	T=0.03
1000Genomes_30x	Global	Study-wide	6404	C=0.9888	T=0.0112
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9605	T=0.0395
1000Genomes_30x	South Asian	Sub	1202	C=0.9925	T=0.0075
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.987	T=0.013
1000Genomes	Global	Study-wide	5008	C=0.9894	T=0.0106
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9622	T=0.0378
1000Genomes	South Asian	Sub	978	C=0.994	T=0.006
1000Genomes	American	Sub	694	C=0.987	T=0.013
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9801	T=0.0199
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9515	T=0.0485
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9625	T=0.0375
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9995	T=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.957	T=0.043
Northern Sweden	ACPOP	Study-wide	600	C=0.953	T=0.047
Qatari	Global	Study-wide	216	C=0.995	T=0.005
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
SGDP_PRJ	Global	Study-wide	8	C=0.4	T=0.6

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.145126363C>T
GRCh37.p13 chr 4	NC_000004.11:g.146047515C>T
ABCE1 RefSeqGene	NG_047075.1:g.33360C>T

Gene: ABCE1, ATP binding cassette subfamily E member 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCE1 transcript variant 2	NM_001040876.2:c.1753-116… NM_001040876.2:c.1753-1163C>T	N/A	Intron Variant
ABCE1 transcript variant 1	NM_002940.3:c.1753-1163C>T	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=	T
GRCh38.p14 chr 4	NC_000004.12:g.145126363=	NC_000004.12:g.145126363C>T
GRCh37.p13 chr 4	NC_000004.11:g.146047515=	NC_000004.11:g.146047515C>T
ABCE1 RefSeqGene	NG_047075.1:g.33360=	NG_047075.1:g.33360C>T
ABCE1 transcript variant 2	NM_001040876.1:c.1753-1163=	NM_001040876.1:c.1753-1163C>T
ABCE1 transcript variant 2	NM_001040876.2:c.1753-1163=	NM_001040876.2:c.1753-1163C>T
ABCE1 transcript variant 1	NM_002940.2:c.1753-1163=	NM_002940.2:c.1753-1163C>T
ABCE1 transcript variant 1	NM_002940.3:c.1753-1163=	NM_002940.3:c.1753-1163C>T

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, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss92817351	Mar 24, 2008 (129)
2	ENSEMBL	ss139941660	Dec 01, 2009 (131)
3	COMPLETE_GENOMICS	ss162632827	Jul 04, 2010 (132)
4	1000GENOMES	ss332021805	May 09, 2011 (134)
5	EVA-GONL	ss980793312	Aug 21, 2014 (142)
6	1000GENOMES	ss1312246974	Aug 21, 2014 (142)
7	EVA_GENOME_DK	ss1580822495	Apr 01, 2015 (144)
8	EVA_DECODE	ss1590305924	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1611396190	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1654390223	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1924035426	Feb 12, 2016 (147)
12	JJLAB	ss2022604076	Sep 14, 2016 (149)
13	HUMAN_LONGEVITY	ss2268015581	Dec 20, 2016 (150)
14	GNOMAD	ss2816501633	Nov 08, 2017 (151)
15	SWEGEN	ss2995732055	Nov 08, 2017 (151)
16	CSHL	ss3346012911	Nov 08, 2017 (151)
17	EGCUT_WGS	ss3663636900	Jul 13, 2019 (153)
18	EVA_DECODE	ss3713269521	Jul 13, 2019 (153)
19	ACPOP	ss3731702682	Jul 13, 2019 (153)
20	SGDP_PRJ	ss3860285253	Apr 26, 2020 (154)
21	KOGIC	ss3955323261	Apr 26, 2020 (154)
22	TOPMED	ss4635775561	Apr 26, 2021 (155)
23	1000G_HIGH_COVERAGE	ss5261400738	Oct 13, 2022 (156)
24	EVA	ss5352984716	Oct 13, 2022 (156)
25	HUGCELL_USP	ss5459914496	Oct 13, 2022 (156)
26	EVA	ss5507772117	Oct 13, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5543697430	Oct 13, 2022 (156)
28	SANFORD_IMAGENETICS	ss5636318033	Oct 13, 2022 (156)
29	EVA	ss5844862169	Oct 13, 2022 (156)
30	EVA	ss5865932225	Oct 13, 2022 (156)
31	EVA	ss5964720204	Oct 13, 2022 (156)
32	1000Genomes	NC_000004.11 - 146047515	Oct 12, 2018 (152)
33	1000Genomes_30x	NC_000004.12 - 145126363	Oct 13, 2022 (156)
34	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 146047515	Oct 12, 2018 (152)
35	Genetic variation in the Estonian population	NC_000004.11 - 146047515	Oct 12, 2018 (152)
36	The Danish reference pan genome	NC_000004.11 - 146047515	Apr 26, 2020 (154)
37	gnomAD - Genomes	NC_000004.12 - 145126363	Apr 26, 2021 (155)
38	Genome of the Netherlands Release 5	NC_000004.11 - 146047515	Apr 26, 2020 (154)
39	Korean Genome Project	NC_000004.12 - 145126363	Apr 26, 2020 (154)
40	Northern Sweden	NC_000004.11 - 146047515	Jul 13, 2019 (153)
41	Qatari	NC_000004.11 - 146047515	Apr 26, 2020 (154)
42	SGDP_PRJ	NC_000004.11 - 146047515	Apr 26, 2020 (154)
43	TopMed	NC_000004.12 - 145126363	Apr 26, 2021 (155)
44	UK 10K study - Twins	NC_000004.11 - 146047515	Oct 12, 2018 (152)
45	ALFA	NC_000004.12 - 145126363	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
ss92817351, ss162632827, ss1590305924	NC_000004.10:146266964:C:T	NC_000004.12:145126362:C:T	(self)
23738574, 13198039, 9375148, 6987434, 5848205, 4987547, 6077356, 12302233, 13198039, ss332021805, ss980793312, ss1312246974, ss1580822495, ss1611396190, ss1654390223, ss1924035426, ss2022604076, ss2816501633, ss2995732055, ss3346012911, ss3663636900, ss3731702682, ss3860285253, ss5352984716, ss5507772117, ss5636318033, ss5844862169, ss5964720204	NC_000004.11:146047514:C:T	NC_000004.12:145126362:C:T	(self)
31223365, 168138627, 11701262, 473153117, 6595292747, ss2268015581, ss3713269521, ss3955323261, ss4635775561, ss5261400738, ss5459914496, ss5543697430, ss5865932225	NC_000004.12:145126362:C:T	NC_000004.12:145126362:C:T	(self)
ss139941660	NT_016354.19:70595235:C:T	NC_000004.12:145126362: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 rs62345101

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

rs62345101