Name: rs201481928
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.

rs201481928

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:110147610-110147618 (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: delTT / delT / dupT
Variation Type: Indel Insertion and Deletion
Frequency: delTT=0.000026 (7/264690, TOPMED)
dupT=0.00018 (4/22220, 14KJPN)
dupT=0.00022 (4/18458, ALFA) (+ 2 more)
dupT=0.0044 (21/4805, 1000G_30x)
dupT=0.0058 (22/3775, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMEM164 : 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	18458	TTTTTTTTT=0.99978	TTTTTTT=0.00000, TTTTTTTT=0.00000, TTTTTTTTTT=0.00022	0.999675	0.000108	0.000217	32
European	Sub	14150	TTTTTTTTT=0.99972	TTTTTTT=0.00000, TTTTTTTT=0.00000, TTTTTTTTTT=0.00028	0.999576	0.000141	0.000283	32
African	Sub	2842	TTTTTTTTT=1.0000	TTTTTTT=0.0000, TTTTTTTT=0.0000, TTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	114	TTTTTTTTT=1.000	TTTTTTT=0.000, TTTTTTTT=0.000, TTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
African American	Sub	2728	TTTTTTTTT=1.0000	TTTTTTT=0.0000, TTTTTTTT=0.0000, TTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	112	TTTTTTTTT=1.000	TTTTTTT=0.000, TTTTTTTT=0.000, TTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	86	TTTTTTTTT=1.00	TTTTTTT=0.00, TTTTTTTT=0.00, TTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	TTTTTTTTT=1.00	TTTTTTT=0.00, TTTTTTTT=0.00, TTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	142	TTTTTTTTT=1.000	TTTTTTT=0.000, TTTTTTTT=0.000, TTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	610	TTTTTTTTT=1.000	TTTTTTT=0.000, TTTTTTTT=0.000, TTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	98	TTTTTTTTT=1.00	TTTTTTT=0.00, TTTTTTTT=0.00, TTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other	Sub	504	TTTTTTTTT=1.000	TTTTTTT=0.000, TTTTTTTT=0.000, TTTTTTTTTT=0.000	1.0	0.0	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	(T)₉=0.999974	delTT=0.000026
14KJPN	JAPANESE	Study-wide	22220	- No frequency provided	dupT=0.00018
Allele Frequency Aggregator	Total	Global	18458	(T)₉=0.99978	delTT=0.00000, delT=0.00000, dupT=0.00022
Allele Frequency Aggregator	European	Sub	14150	(T)₉=0.99972	delTT=0.00000, delT=0.00000, dupT=0.00028
Allele Frequency Aggregator	African	Sub	2842	(T)₉=1.0000	delTT=0.0000, delT=0.0000, dupT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(T)₉=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Other	Sub	504	(T)₉=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	142	(T)₉=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Asian	Sub	112	(T)₉=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(T)₉=1.00	delTT=0.00, delT=0.00, dupT=0.00
1000Genomes_30x	Global	Study-wide	4805	- No frequency provided	dupT=0.0044
1000Genomes_30x	African	Sub	1328	- No frequency provided	dupT=0.0120
1000Genomes_30x	Europe	Sub	961	- No frequency provided	dupT=0.000
1000Genomes_30x	South Asian	Sub	883	- No frequency provided	dupT=0.001
1000Genomes_30x	East Asian	Sub	878	- No frequency provided	dupT=0.000
1000Genomes_30x	American	Sub	755	- No frequency provided	dupT=0.005
1000Genomes	Global	Study-wide	3775	- No frequency provided	dupT=0.0058
1000Genomes	African	Sub	1003	- No frequency provided	dupT=0.0130
1000Genomes	Europe	Sub	766	- No frequency provided	dupT=0.000
1000Genomes	East Asian	Sub	764	- No frequency provided	dupT=0.004
1000Genomes	South Asian	Sub	718	- No frequency provided	dupT=0.003
1000Genomes	American	Sub	524	- No frequency provided	dupT=0.008

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 X	NC_000023.11:g.110147617_110147618del
GRCh38.p14 chr X	NC_000023.11:g.110147618del
GRCh38.p14 chr X	NC_000023.11:g.110147618dup
GRCh37.p13 chr X	NC_000023.10:g.109390845_109390846del
GRCh37.p13 chr X	NC_000023.10:g.109390846del
GRCh37.p13 chr X	NC_000023.10:g.109390846dup

Gene: TMEM164, transmembrane protein 164 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM164 transcript variant 5	NM_001353849.2:c.586+2741… NM_001353849.2:c.586+2741_586+2742del	N/A	Intron Variant
TMEM164 transcript variant 4	NM_001353850.2:c.205+2741… NM_001353850.2:c.205+2741_205+2742del	N/A	Intron Variant
TMEM164 transcript variant 3	NM_001353851.2:c.205+2741… NM_001353851.2:c.205+2741_205+2742del	N/A	Intron Variant
TMEM164 transcript variant 1	NM_017698.3:c.139+2741_13… NM_017698.3:c.139+2741_139+2742del	N/A	Intron Variant
TMEM164 transcript variant 2	NM_032227.4:c.586+2741_58… NM_032227.4:c.586+2741_586+2742del	N/A	Intron Variant
TMEM164 transcript variant X2	XM_005262205.5:c.586+2741… XM_005262205.5:c.586+2741_586+2742del	N/A	Intron Variant
TMEM164 transcript variant X4	XM_005262208.6:c.280+2741… XM_005262208.6:c.280+2741_280+2742del	N/A	Intron Variant
TMEM164 transcript variant X11	XM_011531055.3:c.139+2741… XM_011531055.3:c.139+2741_139+2742del	N/A	Intron Variant
TMEM164 transcript variant X6	XM_017029894.3:c.229+2741… XM_017029894.3:c.229+2741_229+2742del	N/A	Intron Variant
TMEM164 transcript variant X10	XM_017029897.2:c.199+2741… XM_017029897.2:c.199+2741_199+2742del	N/A	Intron Variant
TMEM164 transcript variant X8	XM_017029899.2:c.205+2741… XM_017029899.2:c.205+2741_205+2742del	N/A	Intron Variant
TMEM164 transcript variant X1	XM_047442565.1:c.586+2741… XM_047442565.1:c.586+2741_586+2742del	N/A	Intron Variant
TMEM164 transcript variant X3	XM_047442566.1:c.469+2741… XM_047442566.1:c.469+2741_469+2742del	N/A	Intron Variant
TMEM164 transcript variant X4	XM_047442567.1:c.469+2741… XM_047442567.1:c.469+2741_469+2742del	N/A	Intron Variant
TMEM164 transcript variant X5	XM_047442568.1:c.280+2741… XM_047442568.1:c.280+2741_280+2742del	N/A	Intron Variant
TMEM164 transcript variant X7	XM_047442569.1:c.205+2741… XM_047442569.1:c.205+2741_205+2742del	N/A	Intron Variant
TMEM164 transcript variant X9	XM_047442570.1:c.205+2741… XM_047442570.1:c.205+2741_205+2742del	N/A	Intron Variant
TMEM164 transcript variant X12	XM_047442571.1:c.139+2741… XM_047442571.1:c.139+2741_139+2742del	N/A	Intron Variant
TMEM164 transcript variant X13	XM_047442572.1:c.139+2741… XM_047442572.1:c.139+2741_139+2742del	N/A	Intron Variant
TMEM164 transcript variant X14	XM_047442573.1:c.88+2741_… XM_047442573.1:c.88+2741_88+2742del	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	(T)₉=	delTT	delT	dupT
GRCh38.p14 chr X	NC_000023.11:g.110147610_110147618=	NC_000023.11:g.110147617_110147618del	NC_000023.11:g.110147618del	NC_000023.11:g.110147618dup
GRCh37.p13 chr X	NC_000023.10:g.109390838_109390846=	NC_000023.10:g.109390845_109390846del	NC_000023.10:g.109390846del	NC_000023.10:g.109390846dup
TMEM164 transcript variant 5	NM_001353849.2:c.586+2734=	NM_001353849.2:c.586+2741_586+2742del	NM_001353849.2:c.586+2742del	NM_001353849.2:c.586+2742dup
TMEM164 transcript variant 4	NM_001353850.2:c.205+2734=	NM_001353850.2:c.205+2741_205+2742del	NM_001353850.2:c.205+2742del	NM_001353850.2:c.205+2742dup
TMEM164 transcript variant 3	NM_001353851.2:c.205+2734=	NM_001353851.2:c.205+2741_205+2742del	NM_001353851.2:c.205+2742del	NM_001353851.2:c.205+2742dup
TMEM164 transcript variant 1	NM_017698.2:c.139+2734=	NM_017698.2:c.139+2741_139+2742del	NM_017698.2:c.139+2742del	NM_017698.2:c.139+2742dup
TMEM164 transcript variant 1	NM_017698.3:c.139+2734=	NM_017698.3:c.139+2741_139+2742del	NM_017698.3:c.139+2742del	NM_017698.3:c.139+2742dup
TMEM164 transcript variant 2	NM_032227.3:c.586+2734=	NM_032227.3:c.586+2741_586+2742del	NM_032227.3:c.586+2742del	NM_032227.3:c.586+2742dup
TMEM164 transcript variant 2	NM_032227.4:c.586+2734=	NM_032227.4:c.586+2741_586+2742del	NM_032227.4:c.586+2742del	NM_032227.4:c.586+2742dup
TMEM164 transcript variant X1	XM_005262205.1:c.586+2734=	XM_005262205.1:c.586+2741_586+2742del	XM_005262205.1:c.586+2742del	XM_005262205.1:c.586+2742dup
TMEM164 transcript variant X2	XM_005262205.5:c.586+2734=	XM_005262205.5:c.586+2741_586+2742del	XM_005262205.5:c.586+2742del	XM_005262205.5:c.586+2742dup
TMEM164 transcript variant X2	XM_005262206.1:c.586+2734=	XM_005262206.1:c.586+2741_586+2742del	XM_005262206.1:c.586+2742del	XM_005262206.1:c.586+2742dup
TMEM164 transcript variant X3	XM_005262207.1:c.469+2734=	XM_005262207.1:c.469+2741_469+2742del	XM_005262207.1:c.469+2742del	XM_005262207.1:c.469+2742dup
TMEM164 transcript variant X4	XM_005262208.1:c.280+2734=	XM_005262208.1:c.280+2741_280+2742del	XM_005262208.1:c.280+2742del	XM_005262208.1:c.280+2742dup
TMEM164 transcript variant X4	XM_005262208.6:c.280+2734=	XM_005262208.6:c.280+2741_280+2742del	XM_005262208.6:c.280+2742del	XM_005262208.6:c.280+2742dup
TMEM164 transcript variant X5	XM_005262209.1:c.148+2734=	XM_005262209.1:c.148+2741_148+2742del	XM_005262209.1:c.148+2742del	XM_005262209.1:c.148+2742dup
TMEM164 transcript variant X6	XM_005262210.1:c.139+2734=	XM_005262210.1:c.139+2741_139+2742del	XM_005262210.1:c.139+2742del	XM_005262210.1:c.139+2742dup
TMEM164 transcript variant X7	XM_005262211.1:c.139+2734=	XM_005262211.1:c.139+2741_139+2742del	XM_005262211.1:c.139+2742del	XM_005262211.1:c.139+2742dup
TMEM164 transcript variant X11	XM_011531055.3:c.139+2734=	XM_011531055.3:c.139+2741_139+2742del	XM_011531055.3:c.139+2742del	XM_011531055.3:c.139+2742dup
TMEM164 transcript variant X6	XM_017029894.3:c.229+2734=	XM_017029894.3:c.229+2741_229+2742del	XM_017029894.3:c.229+2742del	XM_017029894.3:c.229+2742dup
TMEM164 transcript variant X10	XM_017029897.2:c.199+2734=	XM_017029897.2:c.199+2741_199+2742del	XM_017029897.2:c.199+2742del	XM_017029897.2:c.199+2742dup
TMEM164 transcript variant X8	XM_017029899.2:c.205+2734=	XM_017029899.2:c.205+2741_205+2742del	XM_017029899.2:c.205+2742del	XM_017029899.2:c.205+2742dup
TMEM164 transcript variant X1	XM_047442565.1:c.586+2734=	XM_047442565.1:c.586+2741_586+2742del	XM_047442565.1:c.586+2742del	XM_047442565.1:c.586+2742dup
TMEM164 transcript variant X3	XM_047442566.1:c.469+2734=	XM_047442566.1:c.469+2741_469+2742del	XM_047442566.1:c.469+2742del	XM_047442566.1:c.469+2742dup
TMEM164 transcript variant X4	XM_047442567.1:c.469+2734=	XM_047442567.1:c.469+2741_469+2742del	XM_047442567.1:c.469+2742del	XM_047442567.1:c.469+2742dup
TMEM164 transcript variant X5	XM_047442568.1:c.280+2734=	XM_047442568.1:c.280+2741_280+2742del	XM_047442568.1:c.280+2742del	XM_047442568.1:c.280+2742dup
TMEM164 transcript variant X7	XM_047442569.1:c.205+2734=	XM_047442569.1:c.205+2741_205+2742del	XM_047442569.1:c.205+2742del	XM_047442569.1:c.205+2742dup
TMEM164 transcript variant X9	XM_047442570.1:c.205+2734=	XM_047442570.1:c.205+2741_205+2742del	XM_047442570.1:c.205+2742del	XM_047442570.1:c.205+2742dup
TMEM164 transcript variant X12	XM_047442571.1:c.139+2734=	XM_047442571.1:c.139+2741_139+2742del	XM_047442571.1:c.139+2742del	XM_047442571.1:c.139+2742dup
TMEM164 transcript variant X13	XM_047442572.1:c.139+2734=	XM_047442572.1:c.139+2741_139+2742del	XM_047442572.1:c.139+2742del	XM_047442572.1:c.139+2742dup
TMEM164 transcript variant X14	XM_047442573.1:c.88+2734=	XM_047442573.1:c.88+2741_88+2742del	XM_047442573.1:c.88+2742del	XM_047442573.1:c.88+2742dup

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#.

13 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss500071162	May 04, 2012 (137)
2	1000GENOMES	ss1555720403	Apr 01, 2015 (144)
3	KHV_HUMAN_GENOMES	ss3823284381	Jul 14, 2019 (153)
4	GNOMAD	ss4376885616	Apr 27, 2021 (155)
5	GNOMAD	ss4376885617	Apr 27, 2021 (155)
6	GNOMAD	ss4376885618	Apr 27, 2021 (155)
7	TOPMED	ss5133832300	Apr 27, 2021 (155)
8	1000G_HIGH_COVERAGE	ss5313570623	Oct 17, 2022 (156)
9	HUGCELL_USP	ss5505026548	Oct 17, 2022 (156)
10	1000G_HIGH_COVERAGE	ss5622462764	Oct 17, 2022 (156)
11	SANFORD_IMAGENETICS	ss5665710291	Oct 17, 2022 (156)
12	TOMMO_GENOMICS	ss5798082816	Oct 17, 2022 (156)
13	EVA	ss5978801548	Oct 17, 2022 (156)
14	1000Genomes	NC_000023.10 - 109390838	Oct 12, 2018 (152)
15	1000Genomes_30x	NC_000023.11 - 110147610	Oct 17, 2022 (156)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 588746259 (NC_000023.11:110147609::T 425/101890) Row 588746260 (NC_000023.11:110147609:T: 6/101903) Row 588746261 (NC_000023.11:110147609:TT: 7/101906)	-	Apr 27, 2021 (155)
17	gnomAD - Genomes Submission ignored due to conflicting rows: Row 588746259 (NC_000023.11:110147609::T 425/101890) Row 588746260 (NC_000023.11:110147609:T: 6/101903) Row 588746261 (NC_000023.11:110147609:TT: 7/101906)	-	Apr 27, 2021 (155)
18	gnomAD - Genomes Submission ignored due to conflicting rows: Row 588746259 (NC_000023.11:110147609::T 425/101890) Row 588746260 (NC_000023.11:110147609:T: 6/101903) Row 588746261 (NC_000023.11:110147609:TT: 7/101906)	-	Apr 27, 2021 (155)
19	14KJPN	NC_000023.11 - 110147610	Oct 17, 2022 (156)
20	TopMed	NC_000023.11 - 110147610	Apr 27, 2021 (155)
21	ALFA	NC_000023.11 - 110147610	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
697438657, ss4376885618, ss5133832300	NC_000023.11:110147609:TT:	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTT	(self)
3438703344	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTT	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTT	(self)
ss4376885617	NC_000023.11:110147609:T:	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTT	(self)
3438703344	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTT	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTT	(self)
83683213, ss500071162, ss1555720403, ss5665710291, ss5978801548	NC_000023.10:109390837::T	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTTTT	(self)
109988699, 131919920, ss3823284381, ss4376885616, ss5313570623, ss5505026548, ss5622462764, ss5798082816	NC_000023.11:110147609::T	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTTTT	(self)
3438703344	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTTTT	NC_000023.11:110147609:TTTTTTTTT:T… NC_000023.11:110147609:TTTTTTTTT:TTTTTTTTTT	(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 rs201481928

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.
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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs201481928