Name: rs60591499
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.

rs60591499

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:25430701-25430703 (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: delC
Variation Type: Indel Insertion and Deletion
Frequency: delC=0.004904 (1298/264690, TOPMED)
delC=0.002924 (410/140210, GnomAD)
delC=0.18975 (5362/28258, 14KJPN) (+ 7 more)
delC=0.18950 (3176/16760, 8.3KJPN)
delC=0.00135 (19/14050, ALFA)
delC=0.0250 (160/6404, 1000G_30x)
delC=0.0196 (98/5008, 1000G)
delC=0.0005 (2/3854, ALSPAC)
delC=0.0000 (0/3708, TWINSUK)
delC=0.071 (15/212, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MACO1 : 2KB Upstream Variant
RHCE : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	14050	CCC=0.99865	CC=0.00135
European	Sub	9690	CCC=0.9999	CC=0.0001
African	Sub	2898	CCC=1.0000	CC=0.0000
African Others	Sub	114	CCC=1.000	CC=0.000
African American	Sub	2784	CCC=1.0000	CC=0.0000
Asian	Sub	112	CCC=0.893	CC=0.107
East Asian	Sub	86	CCC=0.86	CC=0.14
Other Asian	Sub	26	CCC=1.00	CC=0.00
Latin American 1	Sub	146	CCC=1.000	CC=0.000
Latin American 2	Sub	610	CCC=1.000	CC=0.000
South Asian	Sub	98	CCC=1.00	CC=0.00
Other	Sub	496	CCC=0.988	CC=0.012

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	CCC=0.995096	delC=0.004904
gnomAD - Genomes	Global	Study-wide	140210	CCC=0.997076	delC=0.002924
gnomAD - Genomes	European	Sub	75934	CCC=0.99995	delC=0.00005
gnomAD - Genomes	African	Sub	42020	CCC=0.99990	delC=0.00010
gnomAD - Genomes	American	Sub	13658	CCC=0.99971	delC=0.00029
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	CCC=1.0000	delC=0.0000
gnomAD - Genomes	East Asian	Sub	3128	CCC=0.8782	delC=0.1218
gnomAD - Genomes	Other	Sub	2150	CCC=0.9921	delC=0.0079
14KJPN	JAPANESE	Study-wide	28258	CCC=0.81025	delC=0.18975
8.3KJPN	JAPANESE	Study-wide	16760	CCC=0.81050	delC=0.18950
Allele Frequency Aggregator	Total	Global	14050	CCC=0.99865	delC=0.00135
Allele Frequency Aggregator	European	Sub	9690	CCC=0.9999	delC=0.0001
Allele Frequency Aggregator	African	Sub	2898	CCC=1.0000	delC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	CCC=1.000	delC=0.000
Allele Frequency Aggregator	Other	Sub	496	CCC=0.988	delC=0.012
Allele Frequency Aggregator	Latin American 1	Sub	146	CCC=1.000	delC=0.000
Allele Frequency Aggregator	Asian	Sub	112	CCC=0.893	delC=0.107
Allele Frequency Aggregator	South Asian	Sub	98	CCC=1.00	delC=0.00
1000Genomes_30x	Global	Study-wide	6404	CCC=0.9750	delC=0.0250
1000Genomes_30x	African	Sub	1786	CCC=1.0000	delC=0.0000
1000Genomes_30x	Europe	Sub	1266	CCC=1.0000	delC=0.0000
1000Genomes_30x	South Asian	Sub	1202	CCC=0.9950	delC=0.0050
1000Genomes_30x	East Asian	Sub	1170	CCC=0.8684	delC=0.1316
1000Genomes_30x	American	Sub	980	CCC=1.000	delC=0.000
1000Genomes	Global	Study-wide	5008	CCC=0.9804	delC=0.0196
1000Genomes	African	Sub	1322	CCC=1.0000	delC=0.0000
1000Genomes	East Asian	Sub	1008	CCC=0.9058	delC=0.0942
1000Genomes	Europe	Sub	1006	CCC=1.0000	delC=0.0000
1000Genomes	South Asian	Sub	978	CCC=0.997	delC=0.003
1000Genomes	American	Sub	694	CCC=1.000	delC=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	CCC=0.9995	delC=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	CCC=1.0000	delC=0.0000
A Vietnamese Genetic Variation Database	Global	Study-wide	212	CCC=0.929	delC=0.071

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.25430703del
GRCh37.p13 chr 1	NC_000001.10:g.25757194del
RHCE RefSeqGene (LRG_797)	NG_009208.3:g.4492del

Gene: MACO1, macoilin 1 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MACO1 transcript variant 2	NM_001282564.2:c.	N/A	Upstream Transcript Variant
MACO1 transcript variant 1	NM_018202.6:c.	N/A	Upstream Transcript Variant
MACO1 transcript variant X1	XM_005245931.3:c.	N/A	Upstream Transcript Variant

Gene: RHCE, Rh blood group CcEe antigens (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RHCE transcript variant 5	NM_001330430.4:c.	N/A	N/A
RHCE transcript variant 1	NM_020485.8:c.	N/A	N/A
RHCE transcript variant 3	NM_138616.5:c.	N/A	N/A
RHCE transcript variant 4	NM_138617.5:c.	N/A	N/A
RHCE transcript variant 2	NM_138618.6:c.	N/A	N/A
RHCE transcript variant X2	XM_011541889.4:c.	N/A	Upstream Transcript Variant
RHCE transcript variant X3	XM_047427028.1:c.	N/A	Upstream Transcript Variant
RHCE transcript variant X5	XM_005245957.5:c.	N/A	N/A
RHCE transcript variant X4	XM_006710810.4:c.	N/A	N/A
RHCE transcript variant X1	XM_011541888.4:c.	N/A	N/A
RHCE transcript variant X6	XM_017002014.3:c.	N/A	N/A

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	CCC=	delC
GRCh38.p14 chr 1	NC_000001.11:g.25430701_25430703=	NC_000001.11:g.25430703del
GRCh37.p13 chr 1	NC_000001.10:g.25757192_25757194=	NC_000001.10:g.25757194del
RHCE RefSeqGene (LRG_797)	NG_009208.3:g.4490_4492=	NG_009208.3:g.4492del

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#.

26 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss82311989	Sep 08, 2015 (146)
2	HGSV	ss82329848	Sep 08, 2015 (146)
3	GMI	ss154529515	Dec 01, 2009 (137)
4	GMI	ss287960602	May 04, 2012 (137)
5	1000GENOMES	ss326016250	May 09, 2011 (137)
6	1000GENOMES	ss498810466	May 04, 2012 (137)
7	LUNTER	ss552752203	Apr 25, 2013 (138)
8	SSMP	ss663178152	Apr 01, 2015 (144)
9	1000GENOMES	ss1367675102	Aug 21, 2014 (142)
10	EVA_UK10K_ALSPAC	ss1700393268	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1700393270	Apr 01, 2015 (144)
12	GNOMAD	ss2752833141	Nov 08, 2017 (151)
13	MCHAISSO	ss3063581331	Nov 08, 2017 (151)
14	EVA_DECODE	ss3686376456	Jul 12, 2019 (153)
15	KHV_HUMAN_GENOMES	ss3798978521	Jul 12, 2019 (153)
16	TOPMED	ss4442628613	Apr 27, 2021 (155)
17	TOMMO_GENOMICS	ss5143000219	Apr 27, 2021 (155)
18	1000G_HIGH_COVERAGE	ss5241561048	Oct 13, 2022 (156)
19	HUGCELL_USP	ss5442704825	Oct 13, 2022 (156)
20	1000G_HIGH_COVERAGE	ss5513494006	Oct 13, 2022 (156)
21	SANFORD_IMAGENETICS	ss5625141116	Oct 13, 2022 (156)
22	TOMMO_GENOMICS	ss5667463419	Oct 13, 2022 (156)
23	YY_MCH	ss5800425167	Oct 13, 2022 (156)
24	EVA	ss5848828520	Oct 13, 2022 (156)
25	EVA	ss5907453978	Oct 13, 2022 (156)
26	EVA	ss5936957311	Oct 13, 2022 (156)
27	1000Genomes	NC_000001.10 - 25757192	Oct 11, 2018 (152)
28	1000Genomes_30x	NC_000001.11 - 25430701	Oct 13, 2022 (156)
29	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 25757192	Oct 11, 2018 (152)
30	gnomAD - Genomes	NC_000001.11 - 25430701	Apr 27, 2021 (155)
31	8.3KJPN	NC_000001.10 - 25757192	Apr 27, 2021 (155)
32	14KJPN	NC_000001.11 - 25430701	Oct 13, 2022 (156)
33	TopMed	NC_000001.11 - 25430701	Apr 27, 2021 (155)
34	UK 10K study - Twins	NC_000001.10 - 25757192	Oct 11, 2018 (152)
35	A Vietnamese Genetic Variation Database	NC_000001.10 - 25757192	Jul 12, 2019 (153)
36	ALFA	NC_000001.11 - 25430701	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).

Associated ID	History Updated (Build)
rs74413746	May 11, 2012 (137)
rs143578689	May 04, 2012 (137)
rs374042557	May 13, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82311989, ss82329848	NC_000001.8:25502509:C:	NC_000001.11:25430700:CCC:CC	(self)
ss287960602, ss326016250, ss552752203	NC_000001.9:25629778:C:	NC_000001.11:25430700:CCC:CC	(self)
782708, 415681, 969526, 415681, 87544, ss498810466, ss663178152, ss1367675102, ss1700393268, ss1700393270, ss2752833141, ss5143000219, ss5625141116, ss5936957311	NC_000001.10:25757191:C:	NC_000001.11:25430700:CCC:CC	(self)
1019941, 5471724, 1300523, 6234948, ss3063581331, ss3686376456, ss3798978521, ss4442628613, ss5241561048, ss5442704825, ss5513494006, ss5667463419, ss5800425167, ss5848828520, ss5907453978	NC_000001.11:25430700:C:	NC_000001.11:25430700:CCC:CC	(self)
13420985803	NC_000001.11:25430700:CCC:CC	NC_000001.11:25430700:CCC:CC	(self)
ss154529515	NT_004610.19:12437279:C:	NC_000001.11:25430700:CCC:CC	(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 rs60591499

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

rs60591499