Name: rs1027868324
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.

rs1027868324

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:72406144-72406150 (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: delA / dupA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.000014 (2/139530, GnomAD)
delA=0.00004 (1/28258, 14KJPN)
delA=0.00005 (1/18520, ALFA) (+ 2 more)
delA=0.00006 (1/16760, 8.3KJPN)
delA=0.0002 (1/4480, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMEM202 : 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	18520	AAAAAAA=0.99995	AAAAAA=0.00005, AAAAAAAA=0.00000	0.999892	0.000108	0
European	Sub	14152	AAAAAAA=0.99993	AAAAAA=0.00007, AAAAAAAA=0.00000	0.999859	0.000141	0
African	Sub	2898	AAAAAAA=1.0000	AAAAAA=0.0000, AAAAAAAA=0.0000	1.0	0.0	N/A
African Others	Sub	114	AAAAAAA=1.000	AAAAAA=0.000, AAAAAAAA=0.000	1.0	0.0	N/A
African American	Sub	2784	AAAAAAA=1.0000	AAAAAA=0.0000, AAAAAAAA=0.0000	1.0	0.0	N/A
Asian	Sub	112	AAAAAAA=1.000	AAAAAA=0.000, AAAAAAAA=0.000	1.0	0.0	N/A
East Asian	Sub	86	AAAAAAA=1.00	AAAAAA=0.00, AAAAAAAA=0.00	1.0	0.0	N/A
Other Asian	Sub	26	AAAAAAA=1.00	AAAAAA=0.00, AAAAAAAA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	AAAAAAA=1.000	AAAAAA=0.000, AAAAAAAA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	AAAAAAA=1.000	AAAAAA=0.000, AAAAAAAA=0.000	1.0	0.0	N/A
South Asian	Sub	98	AAAAAAA=1.00	AAAAAA=0.00, AAAAAAAA=0.00	1.0	0.0	N/A
Other	Sub	504	AAAAAAA=1.000	AAAAAA=0.000, AAAAAAAA=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
gnomAD - Genomes	Global	Study-wide	139530	(A)₇=0.999986	delA=0.000014
gnomAD - Genomes	European	Sub	75588	(A)₇=0.99997	delA=0.00003
gnomAD - Genomes	African	Sub	41796	(A)₇=1.00000	delA=0.00000
gnomAD - Genomes	American	Sub	13572	(A)₇=1.00000	delA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	(A)₇=1.0000	delA=0.0000
gnomAD - Genomes	East Asian	Sub	3112	(A)₇=1.0000	delA=0.0000
gnomAD - Genomes	Other	Sub	2142	(A)₇=1.0000	delA=0.0000
14KJPN	JAPANESE	Study-wide	28258	(A)₇=0.99996	delA=0.00004
Allele Frequency Aggregator	Total	Global	18520	(A)₇=0.99995	delA=0.00005, dupA=0.00000
Allele Frequency Aggregator	European	Sub	14152	(A)₇=0.99993	delA=0.00007, dupA=0.00000
Allele Frequency Aggregator	African	Sub	2898	(A)₇=1.0000	delA=0.0000, dupA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₇=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Other	Sub	504	(A)₇=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₇=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₇=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₇=1.00	delA=0.00, dupA=0.00
8.3KJPN	JAPANESE	Study-wide	16760	(A)₇=0.99994	delA=0.00006
Genetic variation in the Estonian population	Estonian	Study-wide	4480	(A)₇=0.9998	delA=0.0002

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 15	NC_000015.10:g.72406150del
GRCh38.p14 chr 15	NC_000015.10:g.72406150dup
GRCh37.p13 chr 15	NC_000015.9:g.72698491del
GRCh37.p13 chr 15	NC_000015.9:g.72698491dup

Gene: TMEM202, transmembrane protein 202 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM202 transcript variant 1	NM_001080462.3:c.338-452d… NM_001080462.3:c.338-452del	N/A	Intron Variant
TMEM202 transcript variant 2	NR_148418.2:n.	N/A	Intron Variant
TMEM202 transcript variant 3	NR_148419.2:n.	N/A	Intron Variant
TMEM202 transcript variant X1	XM_011521497.3:c.221-452d… XM_011521497.3:c.221-452del	N/A	Intron Variant
TMEM202 transcript variant X3	XM_011521499.3:c.4+111del	N/A	Intron Variant
TMEM202 transcript variant X2	XM_024449910.2:c.338-452d… XM_024449910.2:c.338-452del	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	(A)₇=	delA	dupA
GRCh38.p14 chr 15	NC_000015.10:g.72406144_72406150=	NC_000015.10:g.72406150del	NC_000015.10:g.72406150dup
GRCh37.p13 chr 15	NC_000015.9:g.72698485_72698491=	NC_000015.9:g.72698491del	NC_000015.9:g.72698491dup
TMEM202 transcript	NM_001080462.1:c.338-458=	NM_001080462.1:c.338-452del	NM_001080462.1:c.338-452dup
TMEM202 transcript variant 1	NM_001080462.3:c.338-458=	NM_001080462.3:c.338-452del	NM_001080462.3:c.338-452dup
TMEM202 transcript variant X1	XM_011521497.3:c.221-458=	XM_011521497.3:c.221-452del	XM_011521497.3:c.221-452dup
TMEM202 transcript variant X3	XM_011521499.3:c.4+105=	XM_011521499.3:c.4+111del	XM_011521499.3:c.4+111dup
TMEM202 transcript variant X2	XM_024449910.2:c.338-458=	XM_024449910.2:c.338-452del	XM_024449910.2:c.338-452dup

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#.

7 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2936621988	Nov 08, 2017 (151)
2	SWEGEN	ss3013525230	Nov 08, 2017 (151)
3	EGCUT_WGS	ss3680673140	Jul 13, 2019 (153)
4	TOPMED	ss4996672862	Apr 27, 2021 (155)
5	TOPMED	ss4996672863	Apr 27, 2021 (155)
6	TOMMO_GENOMICS	ss5216891492	Apr 27, 2021 (155)
7	TOMMO_GENOMICS	ss5770905319	Oct 16, 2022 (156)
8	Genetic variation in the Estonian population	NC_000015.9 - 72698485	Oct 12, 2018 (152)
9	gnomAD - Genomes	NC_000015.10 - 72406144	Apr 27, 2021 (155)
10	8.3KJPN	NC_000015.9 - 72698485	Apr 27, 2021 (155)
11	14KJPN	NC_000015.10 - 72406144	Oct 16, 2022 (156)
12	TopMed Submission ignored due to conflicting rows: Row 212218522 (NC_000015.10:72406143::A 1/264690) Row 212218523 (NC_000015.10:72406143:A: 1/264690)	-	Apr 27, 2021 (155)
13	TopMed Submission ignored due to conflicting rows: Row 212218522 (NC_000015.10:72406143::A 1/264690) Row 212218523 (NC_000015.10:72406143:A: 1/264690)	-	Apr 27, 2021 (155)
14	ALFA	NC_000015.10 - 72406144	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
26411388, 74860799, ss2936621988, ss3680673140, ss5216891492	NC_000015.9:72698484:A:	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAA	(self)
473469768, 104742423, ss4996672863, ss5770905319	NC_000015.10:72406143:A:	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAA	(self)
4514462112	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAA	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAA	(self)
ss3013525230	NC_000015.9:72698484::A	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAAAA	(self)
ss4996672862	NC_000015.10:72406143::A	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAAAA	(self)
4514462112	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAAAA	NC_000015.10:72406143:AAAAAAA:AAAA… NC_000015.10:72406143:AAAAAAA:AAAAAAAA	(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 rs1027868324

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

rs1027868324