Name: rs145884228
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.

rs145884228

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:40726215-40726227 (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 / dupAT / dupATAT / dup(AT)₃
Variation Type: Indel Insertion and Deletion
Frequency: dupAT=0.09615 (1063/11056, ALFA)
dupAT=0.3337 (1671/5008, 1000G)
dupAT=0.257 (256/998, GoNL) (+ 3 more)
dupAT=0.255 (153/600, NorthernSweden)
(TA)₆T=0.413 (85/206, Vietnamese)
dupAT=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PTGER4 : Intron Variant
TTC33 : 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	Alt HMOZ	HTRZ	HWEP
Total	Global	11056	TATATATATATAT=0.90385	TATATATATATATAT=0.09615, TATATATATATATATAT=0.00000	0.831223	0.023517	0.14526	32
European	Sub	9178	TATATATATATAT=0.8845	TATATATATATATAT=0.1155, TATATATATATATATAT=0.0000	0.797124	0.028111	0.174766	32
African	Sub	1050	TATATATATATAT=1.0000	TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	40	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
African American	Sub	1010	TATATATATATAT=1.0000	TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	44	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	30	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	14	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	90	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	392	TATATATATATAT=1.000	TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	44	TATATATATATAT=1.00	TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Other	Sub	258	TATATATATATAT=0.988	TATATATATATATAT=0.012, TATATATATATATATAT=0.000	0.984496	0.007752	0.007752	30

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
Allele Frequency Aggregator	Total	Global	11056	(TA)₆T=0.90385	dupAT=0.09615, dupATAT=0.00000
Allele Frequency Aggregator	European	Sub	9178	(TA)₆T=0.8845	dupAT=0.1155, dupATAT=0.0000
Allele Frequency Aggregator	African	Sub	1050	(TA)₆T=1.0000	dupAT=0.0000, dupATAT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	392	(TA)₆T=1.000	dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Other	Sub	258	(TA)₆T=0.988	dupAT=0.012, dupATAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	90	(TA)₆T=1.00	dupAT=0.00, dupATAT=0.00
Allele Frequency Aggregator	South Asian	Sub	44	(TA)₆T=1.00	dupAT=0.00, dupATAT=0.00
Allele Frequency Aggregator	Asian	Sub	44	(TA)₆T=1.00	dupAT=0.00, dupATAT=0.00
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupAT=0.3337
1000Genomes	African	Sub	1322	- No frequency provided	dupAT=0.3835
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupAT=0.4752
1000Genomes	Europe	Sub	1006	- No frequency provided	dupAT=0.2306
1000Genomes	South Asian	Sub	978	- No frequency provided	dupAT=0.306
1000Genomes	American	Sub	694	- No frequency provided	dupAT=0.222
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupAT=0.257
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupAT=0.255
A Vietnamese Genetic Variation Database	Global	Study-wide	206	- No frequency provided	dupAT=0.587
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupAT=0.23

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 5	NC_000005.10:g.40726216AT[5]
GRCh38.p14 chr 5	NC_000005.10:g.40726216AT[7]
GRCh38.p14 chr 5	NC_000005.10:g.40726216AT[8]
GRCh38.p14 chr 5	NC_000005.10:g.40726216AT[9]
GRCh37.p13 chr 5	NC_000005.9:g.40726318AT[5]
GRCh37.p13 chr 5	NC_000005.9:g.40726318AT[7]
GRCh37.p13 chr 5	NC_000005.9:g.40726318AT[8]
GRCh37.p13 chr 5	NC_000005.9:g.40726318AT[9]
PTGER4 RefSeqGene	NG_047000.1:g.51719AT[5]
PTGER4 RefSeqGene	NG_047000.1:g.51719AT[7]
PTGER4 RefSeqGene	NG_047000.1:g.51719AT[8]
PTGER4 RefSeqGene	NG_047000.1:g.51719AT[9]

Gene: TTC33, tetratricopeptide repeat domain 33 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TTC33 transcript	NM_012382.3:c.435+2119TA[… NM_012382.3:c.435+2119TA[5]	N/A	Intron Variant
TTC33 transcript variant X1	XM_011514003.4:c.435+2119… XM_011514003.4:c.435+2119TA[5]	N/A	Intron Variant

Gene: PTGER4, prostaglandin E receptor 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTGER4 transcript	NM_000958.3:c.	N/A	Genic Downstream Transcript Variant
PTGER4 transcript variant X3	XM_017009659.3:c.38-1426… XM_017009659.3:c.38-14269TA[5]	N/A	Intron Variant
PTGER4 transcript variant X1	XM_047417413.1:c.	N/A	Genic Downstream Transcript Variant
PTGER4 transcript variant X2	XM_047417414.1:c.	N/A	Genic Downstream Transcript Variant
PTGER4 transcript variant X4	XM_047417415.1:c.	N/A	Genic Downstream Transcript Variant
PTGER4 transcript variant X5	XM_047417416.1:c.	N/A	Genic Downstream 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	(TA)₆T=	delAT	dupAT	dupATAT	dup(AT)₃
GRCh38.p14 chr 5	NC_000005.10:g.40726215_40726227=	NC_000005.10:g.40726216AT[5]	NC_000005.10:g.40726216AT[7]	NC_000005.10:g.40726216AT[8]	NC_000005.10:g.40726216AT[9]
GRCh37.p13 chr 5	NC_000005.9:g.40726317_40726329=	NC_000005.9:g.40726318AT[5]	NC_000005.9:g.40726318AT[7]	NC_000005.9:g.40726318AT[8]	NC_000005.9:g.40726318AT[9]
PTGER4 RefSeqGene	NG_047000.1:g.51718_51730=	NG_047000.1:g.51719AT[5]	NG_047000.1:g.51719AT[7]	NG_047000.1:g.51719AT[8]	NG_047000.1:g.51719AT[9]
TTC33 transcript	NM_012382.2:c.435+2130=	NM_012382.2:c.435+2119TA[5]	NM_012382.2:c.435+2119TA[7]	NM_012382.2:c.435+2119TA[8]	NM_012382.2:c.435+2119TA[9]
TTC33 transcript	NM_012382.3:c.435+2130=	NM_012382.3:c.435+2119TA[5]	NM_012382.3:c.435+2119TA[7]	NM_012382.3:c.435+2119TA[8]	NM_012382.3:c.435+2119TA[9]
TTC33 transcript variant X1	XM_005248276.1:c.303+4047=	XM_005248276.1:c.303+4036TA[5]	XM_005248276.1:c.303+4036TA[7]	XM_005248276.1:c.303+4036TA[8]	XM_005248276.1:c.303+4036TA[9]
TTC33 transcript variant X1	XM_011514003.4:c.435+2130=	XM_011514003.4:c.435+2119TA[5]	XM_011514003.4:c.435+2119TA[7]	XM_011514003.4:c.435+2119TA[8]	XM_011514003.4:c.435+2119TA[9]
PTGER4 transcript variant X3	XM_017009659.3:c.*38-14269=	XM_017009659.3:c.*38-14269TA[5]	XM_017009659.3:c.*38-14269TA[7]	XM_017009659.3:c.*38-14269TA[8]	XM_017009659.3:c.*38-14269TA[9]

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#.

44 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss287771520	Dec 06, 2013 (138)
2	GMI	ss288626662	May 04, 2012 (137)
3	1000GENOMES	ss326699885	May 09, 2011 (134)
4	1000GENOMES	ss326906864	May 09, 2011 (134)
5	LUNTER	ss551491951	Apr 25, 2013 (138)
6	LUNTER	ss551644252	Apr 25, 2013 (138)
7	LUNTER	ss553195043	Apr 25, 2013 (138)
8	SSMP	ss663603317	Apr 01, 2015 (144)
9	BILGI_BIOE	ss666307612	Apr 25, 2013 (138)
10	EVA-GONL	ss981481484	Aug 21, 2014 (142)
11	1000GENOMES	ss1373710903	Aug 21, 2014 (142)
12	DDI	ss1536459844	Apr 01, 2015 (144)
13	EVA_GENOME_DK	ss1576502086	Apr 01, 2015 (144)
14	EVA_DECODE	ss1591004595	Oct 12, 2018 (152)
15	EVA_UK10K_TWINSUK	ss1704644854	Jan 10, 2018 (151)
16	EVA_UK10K_ALSPAC	ss1704646252	Jan 10, 2018 (151)
17	EVA_UK10K_ALSPAC	ss1710205793	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1710205794	Apr 01, 2015 (144)
19	JJLAB	ss2030679333	Sep 14, 2016 (149)
20	SWEGEN	ss2996792315	Nov 08, 2017 (151)
21	SWEGEN	ss2996792316	Nov 08, 2017 (151)
22	MCHAISSO	ss3066014248	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3645873606	Oct 12, 2018 (152)
24	EVA_DECODE	ss3714532647	Jul 13, 2019 (153)
25	EVA_DECODE	ss3714532648	Jul 13, 2019 (153)
26	ACPOP	ss3732287228	Jul 13, 2019 (153)
27	PACBIO	ss3785091475	Jul 13, 2019 (153)
28	PACBIO	ss3790500996	Jul 13, 2019 (153)
29	PACBIO	ss3795377459	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3806510741	Jul 13, 2019 (153)
31	EVA	ss3829209919	Apr 26, 2020 (154)
32	GNOMAD	ss4103039837	Apr 26, 2021 (155)
33	GNOMAD	ss4103039838	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5171364433	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5171364435	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5263654197	Oct 13, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5263654199	Oct 13, 2022 (156)
38	HUGCELL_USP	ss5461910743	Oct 13, 2022 (156)
39	TOMMO_GENOMICS	ss5707307800	Oct 13, 2022 (156)
40	TOMMO_GENOMICS	ss5707307802	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5707307803	Oct 13, 2022 (156)
42	EVA	ss5834822339	Oct 13, 2022 (156)
43	EVA	ss5834822340	Oct 13, 2022 (156)
44	EVA	ss5854782145	Oct 13, 2022 (156)
45	1000Genomes	NC_000005.9 - 40726317	Oct 12, 2018 (152)
46	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 14661955 (NC_000005.9:40726316::TA 824/3854) Row 14661956 (NC_000005.9:40726316:TA: 27/3854)	-	Oct 12, 2018 (152)
47	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 14661955 (NC_000005.9:40726316::TA 824/3854) Row 14661956 (NC_000005.9:40726316:TA: 27/3854)	-	Oct 12, 2018 (152)
48	The Danish reference pan genome	NC_000005.9 - 40726317	Apr 26, 2020 (154)
49	gnomAD - Genomes Submission ignored due to conflicting rows: Row 186223412 (NC_000005.10:40726214::TA 43921/137264) Row 186223413 (NC_000005.10:40726214::TATA 18/137366)	-	Apr 26, 2021 (155)
50	gnomAD - Genomes Submission ignored due to conflicting rows: Row 186223412 (NC_000005.10:40726214::TA 43921/137264) Row 186223413 (NC_000005.10:40726214::TATA 18/137366)	-	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000005.9 - 40726317	Apr 26, 2020 (154)
52	Northern Sweden	NC_000005.9 - 40726317	Jul 13, 2019 (153)
53	8.3KJPN Submission ignored due to conflicting rows: Row 29333740 (NC_000005.9:40726316::TA 9721/16760) Row 29333742 (NC_000005.9:40726316::TATA 3/16760)	-	Apr 26, 2021 (155)
54	8.3KJPN Submission ignored due to conflicting rows: Row 29333740 (NC_000005.9:40726316::TA 9721/16760) Row 29333742 (NC_000005.9:40726316::TATA 3/16760)	-	Apr 26, 2021 (155)
55	14KJPN Submission ignored due to conflicting rows: Row 41144904 (NC_000005.10:40726214::TA 16359/28258) Row 41144906 (NC_000005.10:40726214::TATA 6/28258) Row 41144907 (NC_000005.10:40726214::TATATA 1/28258)	-	Oct 13, 2022 (156)
56	14KJPN Submission ignored due to conflicting rows: Row 41144904 (NC_000005.10:40726214::TA 16359/28258) Row 41144906 (NC_000005.10:40726214::TATA 6/28258) Row 41144907 (NC_000005.10:40726214::TATATA 1/28258)	-	Oct 13, 2022 (156)
57	14KJPN Submission ignored due to conflicting rows: Row 41144904 (NC_000005.10:40726214::TA 16359/28258) Row 41144906 (NC_000005.10:40726214::TATA 6/28258) Row 41144907 (NC_000005.10:40726214::TATATA 1/28258)	-	Oct 13, 2022 (156)
58	UK 10K study - Twins Submission ignored due to conflicting rows: Row 14661955 (NC_000005.9:40726316::TA 825/3708) Row 14661956 (NC_000005.9:40726316:TA: 10/3708)	-	Oct 12, 2018 (152)
59	UK 10K study - Twins Submission ignored due to conflicting rows: Row 14661955 (NC_000005.9:40726316::TA 825/3708) Row 14661956 (NC_000005.9:40726316:TA: 10/3708)	-	Oct 12, 2018 (152)
60	A Vietnamese Genetic Variation Database	NC_000005.9 - 40726317	Jul 13, 2019 (153)
61	ALFA	NC_000005.10 - 40726215	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).

Associated ID	History Updated (Build)
rs370082540	May 15, 2013 (138)
rs796323989	Nov 08, 2017 (151)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1704644854, ss1704646252, ss5834822340	NC_000005.9:40726316:TA:	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATAT	(self)
ss3714532647	NC_000005.10:40726214:TA:	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATAT	(self)
ss326699885, ss326906864, ss551491951, ss551644252, ss553195043	NC_000005.8:40762073::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss1591004595	NC_000005.8:40762077::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss288626662	NC_000005.8:40762086::AT	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
26362784, 991532, 6516576, 5572093, 3260357, ss663603317, ss666307612, ss981481484, ss1373710903, ss1536459844, ss1576502086, ss2030679333, ss2996792315, ss3732287228, ss3785091475, ss3790500996, ss3795377459, ss3829209919, ss5171364433, ss5834822339	NC_000005.9:40726316::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss1710205793, ss1710205794	NC_000005.9:40726318::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss3066014248, ss3645873606, ss3806510741, ss4103039837, ss5263654197, ss5461910743, ss5707307800, ss5854782145	NC_000005.10:40726214::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
3486658161	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss3714532648	NC_000005.10:40726216::TA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss287771520	NT_006576.16:40716329::AT	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATAT	(self)
ss2996792316, ss5171364435	NC_000005.9:40726316::TATA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATATAT	(self)
ss4103039838, ss5263654199, ss5707307802	NC_000005.10:40726214::TATA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATATAT	(self)
3486658161	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATATAT	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATATAT	(self)
ss5707307803	NC_000005.10:40726214::TATATA	NC_000005.10:40726214:TATATATATATA… NC_000005.10:40726214:TATATATATATAT:TATATATATATATATATAT

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs145884228

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

rs145884228