Name: rs1491410347
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.

rs1491410347

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:87836411-87836414 (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: delAT
Variation Type: Indel Insertion and Deletion
Frequency: delAT=0.000136 (36/264690, TOPMED)
delAT=0.000135 (18/133682, GnomAD)
delAT=0.00007 (2/28258, 14KJPN) (+ 4 more)
delAT=0.00012 (2/16760, 8.3KJPN)
delAT=0.00008 (1/11862, ALFA)
delAT=0.0016 (10/6404, 1000G_30x)
delAT=0.0022 (4/1832, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MEPE : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	11862	ATAT=0.99992	AT=0.00008	0.999831	0.000169	0
European	Sub	7618	ATAT=1.0000	AT=0.0000	1.0	0.0	N/A
African	Sub	2816	ATAT=1.0000	AT=0.0000	1.0	0.0	N/A
African Others	Sub	108	ATAT=1.000	AT=0.000	1.0	0.0	N/A
African American	Sub	2708	ATAT=1.0000	AT=0.0000	1.0	0.0	N/A
Asian	Sub	108	ATAT=0.991	AT=0.009	0.981481	0.018519	0
East Asian	Sub	84	ATAT=0.99	AT=0.01	0.97619	0.02381	0
Other Asian	Sub	24	ATAT=1.00	AT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	ATAT=1.000	AT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	ATAT=1.000	AT=0.000	1.0	0.0	N/A
South Asian	Sub	94	ATAT=1.00	AT=0.00	1.0	0.0	N/A
Other	Sub	470	ATAT=1.000	AT=0.000	1.0	0.0	N/A

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	ATAT=0.999864	delAT=0.000136
gnomAD - Genomes	Global	Study-wide	133682	ATAT=0.999865	delAT=0.000135
gnomAD - Genomes	European	Sub	73076	ATAT=1.00000	delAT=0.00000
gnomAD - Genomes	African	Sub	39136	ATAT=1.00000	delAT=0.00000
gnomAD - Genomes	American	Sub	13096	ATAT=1.00000	delAT=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3216	ATAT=1.0000	delAT=0.0000
gnomAD - Genomes	East Asian	Sub	3112	ATAT=0.9942	delAT=0.0058
gnomAD - Genomes	Other	Sub	2046	ATAT=1.0000	delAT=0.0000
14KJPN	JAPANESE	Study-wide	28258	ATAT=0.99993	delAT=0.00007
8.3KJPN	JAPANESE	Study-wide	16760	ATAT=0.99988	delAT=0.00012
Allele Frequency Aggregator	Total	Global	11862	ATAT=0.99992	delAT=0.00008
Allele Frequency Aggregator	European	Sub	7618	ATAT=1.0000	delAT=0.0000
Allele Frequency Aggregator	African	Sub	2816	ATAT=1.0000	delAT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	ATAT=1.000	delAT=0.000
Allele Frequency Aggregator	Other	Sub	470	ATAT=1.000	delAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	ATAT=1.000	delAT=0.000
Allele Frequency Aggregator	Asian	Sub	108	ATAT=0.991	delAT=0.009
Allele Frequency Aggregator	South Asian	Sub	94	ATAT=1.00	delAT=0.00
1000Genomes_30x	Global	Study-wide	6404	ATAT=0.9984	delAT=0.0016
1000Genomes_30x	African	Sub	1786	ATAT=1.0000	delAT=0.0000
1000Genomes_30x	Europe	Sub	1266	ATAT=1.0000	delAT=0.0000
1000Genomes_30x	South Asian	Sub	1202	ATAT=0.9975	delAT=0.0025
1000Genomes_30x	East Asian	Sub	1170	ATAT=0.9940	delAT=0.0060
1000Genomes_30x	American	Sub	980	ATAT=1.000	delAT=0.000
Korean Genome Project	KOREAN	Study-wide	1832	ATAT=0.9978	delAT=0.0022

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.87836411AT[1]
GRCh37.p13 chr 4	NC_000004.11:g.88757563AT[1]
MEPE RefSeqGene	NG_034073.1:g.20014AT[1]

Gene: MEPE, matrix extracellular phosphoglycoprotein (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MEPE transcript variant 1	NM_001184694.3:c.54+1645_… NM_001184694.3:c.54+1645_54+1646del	N/A	Intron Variant
MEPE transcript variant 3	NM_001184695.4:c.-392+164… NM_001184695.4:c.-392+1645_-392+1646del	N/A	Intron Variant
MEPE transcript variant 4	NM_001184696.2:c.-414+164… NM_001184696.2:c.-414+1645_-414+1646del	N/A	Intron Variant
MEPE transcript variant 5	NM_001184697.2:c.-485+164… NM_001184697.2:c.-485+1645_-485+1646del	N/A	Intron Variant
MEPE transcript variant 6	NM_001291183.2:c.54+1645_… NM_001291183.2:c.54+1645_54+1646del	N/A	Intron Variant
MEPE transcript variant 2	NM_020203.6:c.54+1645_54+… NM_020203.6:c.54+1645_54+1646del	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	ATAT=	delAT
GRCh38.p14 chr 4	NC_000004.12:g.87836411_87836414=	NC_000004.12:g.87836411AT[1]
GRCh37.p13 chr 4	NC_000004.11:g.88757563_88757566=	NC_000004.11:g.88757563AT[1]
MEPE RefSeqGene	NG_034073.1:g.20014_20017=	NG_034073.1:g.20014AT[1]
MEPE transcript variant 1	NM_001184694.1:c.54+1643=	NM_001184694.1:c.54+1645_54+1646del
MEPE transcript variant 1	NM_001184694.3:c.54+1643=	NM_001184694.3:c.54+1645_54+1646del
MEPE transcript variant 3	NM_001184695.1:c.-392+1643=	NM_001184695.1:c.-392+1645_-392+1646del
MEPE transcript variant 3	NM_001184695.4:c.-392+1643=	NM_001184695.4:c.-392+1645_-392+1646del
MEPE transcript variant 4	NM_001184696.1:c.-414+1643=	NM_001184696.1:c.-414+1645_-414+1646del
MEPE transcript variant 4	NM_001184696.2:c.-414+1643=	NM_001184696.2:c.-414+1645_-414+1646del
MEPE transcript variant 5	NM_001184697.1:c.-485+1643=	NM_001184697.1:c.-485+1645_-485+1646del
MEPE transcript variant 5	NM_001184697.2:c.-485+1643=	NM_001184697.2:c.-485+1645_-485+1646del
MEPE transcript variant 6	NM_001291183.2:c.54+1643=	NM_001291183.2:c.54+1645_54+1646del
MEPE transcript variant 2	NM_020203.3:c.54+1643=	NM_020203.3:c.54+1645_54+1646del
MEPE transcript variant 2	NM_020203.6:c.54+1643=	NM_020203.6:c.54+1645_54+1646del
MEPE transcript variant X1	XM_005263141.1:c.54+1643=	XM_005263141.1:c.54+1645_54+1646del

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#.

10 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2811929988	Jan 10, 2018 (151)
2	EVA_DECODE	ss3712500114	Jul 13, 2019 (153)
3	KOGIC	ss3954599660	Apr 26, 2020 (154)
4	TOPMED	ss4621785842	Apr 26, 2021 (155)
5	TOMMO_GENOMICS	ss5166729059	Apr 26, 2021 (155)
6	1000G_HIGH_COVERAGE	ss5260007032	Oct 13, 2022 (156)
7	1000G_HIGH_COVERAGE	ss5541515075	Oct 13, 2022 (156)
8	TOMMO_GENOMICS	ss5701360829	Oct 13, 2022 (156)
9	YY_MCH	ss5805286023	Oct 13, 2022 (156)
10	EVA	ss5854322530	Oct 13, 2022 (156)
11	1000Genomes_30x	NC_000004.12 - 87836411	Oct 13, 2022 (156)
12	gnomAD - Genomes	NC_000004.12 - 87836411	Apr 26, 2021 (155)
13	Korean Genome Project	NC_000004.12 - 87836411	Apr 26, 2020 (154)
14	8.3KJPN	NC_000004.11 - 88757563	Apr 26, 2021 (155)
15	14KJPN	NC_000004.12 - 87836411	Oct 13, 2022 (156)
16	TopMed	NC_000004.12 - 87836411	Apr 26, 2021 (155)
17	ALFA	NC_000004.12 - 87836411	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
24698366, ss2811929988, ss5166729059	NC_000004.11:88757562:AT:	NC_000004.12:87836410:ATAT:AT	(self)
29041010, 156458506, 10977661, 35197933, 459163398, ss3712500114, ss3954599660, ss4621785842, ss5260007032, ss5541515075, ss5701360829, ss5805286023, ss5854322530	NC_000004.12:87836410:AT:	NC_000004.12:87836410:ATAT:AT	(self)
8786972457	NC_000004.12:87836410:ATAT:AT	NC_000004.12:87836410:ATAT:AT	(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 rs1491410347

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

rs1491410347