Name: rs142641214
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.

rs142641214

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:12138363 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.00106 (52/49210, ALFA)
T=0.00092 (12/12996, GO-ESP)
T=0.0009 (4/4480, Estonian) (+ 4 more)
T=0.0005 (2/3854, ALSPAC)
T=0.0019 (7/3708, TWINSUK)
A=0.0005 (1/1832, Korea1K)
T=0.005 (3/600, NorthernSweden)

Clinical Significance: Reported in ClinVar
Gene : Consequence: TNFRSF8 : Synonymous 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	65446	G=0.99873	A=0.00000, T=0.00127
European	Sub	47188	G=0.99862	A=0.00000, T=0.00138
African	Sub	8382	G=0.9998	A=0.0000, T=0.0002
African Others	Sub	306	G=1.000	A=0.000, T=0.000
African American	Sub	8076	G=0.9998	A=0.0000, T=0.0002
Asian	Sub	168	G=1.000	A=0.000, T=0.000
East Asian	Sub	112	G=1.000	A=0.000, T=0.000
Other Asian	Sub	56	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	500	G=1.000	A=0.000, T=0.000
Latin American 2	Sub	628	G=1.000	A=0.000, T=0.000
South Asian	Sub	98	G=1.00	A=0.00, T=0.00
Other	Sub	8482	G=0.9981	A=0.0000, T=0.0019

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	49210	G=0.99894	A=0.00000, T=0.00106
Allele Frequency Aggregator	European	Sub	37198	G=0.99887	A=0.00000, T=0.00113
Allele Frequency Aggregator	Other	Sub	7060	G=0.9987	A=0.0000, T=0.0013
Allele Frequency Aggregator	African	Sub	3558	G=0.9997	A=0.0000, T=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	628	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, T=0.00
GO Exome Sequencing Project	Global	Study-wide	12996	G=0.99908	T=0.00092
GO Exome Sequencing Project	European American	Sub	8590	G=0.9987	T=0.0013
GO Exome Sequencing Project	African American	Sub	4406	G=0.9998	T=0.0002
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9991	T=0.0009
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9995	T=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9981	T=0.0019
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9995	A=0.0005
Northern Sweden	ACPOP	Study-wide	600	G=0.995	T=0.005

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.12138363G>A
GRCh38.p14 chr 1	NC_000001.11:g.12138363G>T
GRCh37.p13 chr 1	NC_000001.10:g.12198420G>A
GRCh37.p13 chr 1	NC_000001.10:g.12198420G>T
TNFRSF8 RefSeqGene	NG_029573.2:g.79987G>A
TNFRSF8 RefSeqGene	NG_029573.2:g.79987G>T

Gene: TNFRSF8, TNF receptor superfamily member 8 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TNFRSF8 transcript variant 1	NM_001243.5:c.1470G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform 1 precursor	NP_001234.3:p.Pro490=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant 1	NM_001243.5:c.1470G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform 1 precursor	NP_001234.3:p.Pro490=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant 3	NM_001281430.3:c.1134G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform 3	NP_001268359.2:p.Pro378=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant 3	NM_001281430.3:c.1134G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform 3	NP_001268359.2:p.Pro378=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X1	XM_011542441.4:c.1467G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X1	XP_011540743.1:p.Pro489=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X1	XM_011542441.4:c.1467G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X1	XP_011540743.1:p.Pro489=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X2	XM_047434793.1:c.1416G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X2	XP_047290749.1:p.Pro472=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X2	XM_047434793.1:c.1416G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X2	XP_047290749.1:p.Pro472=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X3	XM_047434799.1:c.1413G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X3	XP_047290755.1:p.Pro471=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X3	XM_047434799.1:c.1413G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X3	XP_047290755.1:p.Pro471=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X4	XM_011542443.3:c.1137G>A	P [CCG] > P [CCA]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X4	XP_011540745.1:p.Pro379=	P (Pro) > P (Pro)	Synonymous Variant
TNFRSF8 transcript variant X4	XM_011542443.3:c.1137G>T	P [CCG] > P [CCT]	Coding Sequence Variant
tumor necrosis factor receptor superfamily member 8 isoform X4	XP_011540745.1:p.Pro379=	P (Pro) > P (Pro)	Synonymous 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.

Allele: T (allele ID: 731642 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000907629.3	not provided	Likely-Benign

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	G=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.12138363=	NC_000001.11:g.12138363G>A	NC_000001.11:g.12138363G>T
GRCh37.p13 chr 1	NC_000001.10:g.12198420=	NC_000001.10:g.12198420G>A	NC_000001.10:g.12198420G>T
TNFRSF8 RefSeqGene	NG_029573.2:g.79987=	NG_029573.2:g.79987G>A	NG_029573.2:g.79987G>T
TNFRSF8 transcript variant 1	NM_001243.5:c.1470=	NM_001243.5:c.1470G>A	NM_001243.5:c.1470G>T
TNFRSF8 transcript variant 1	NM_001243.4:c.1470=	NM_001243.4:c.1470G>A	NM_001243.4:c.1470G>T
TNFRSF8 transcript variant 1	NM_001243.3:c.1470=	NM_001243.3:c.1470G>A	NM_001243.3:c.1470G>T
TNFRSF8 transcript variant 3	NM_001281430.3:c.1134=	NM_001281430.3:c.1134G>A	NM_001281430.3:c.1134G>T
TNFRSF8 transcript variant 3	NM_001281430.2:c.1134=	NM_001281430.2:c.1134G>A	NM_001281430.2:c.1134G>T
TNFRSF8 transcript variant 3	NM_001281430.1:c.1134=	NM_001281430.1:c.1134G>A	NM_001281430.1:c.1134G>T
TNFRSF8 transcript variant X1	XM_011542441.4:c.1467=	XM_011542441.4:c.1467G>A	XM_011542441.4:c.1467G>T
TNFRSF8 transcript variant X1	XM_011542441.3:c.1467=	XM_011542441.3:c.1467G>A	XM_011542441.3:c.1467G>T
TNFRSF8 transcript variant X1	XM_011542441.2:c.1467=	XM_011542441.2:c.1467G>A	XM_011542441.2:c.1467G>T
TNFRSF8 transcript variant X1	XM_011542441.1:c.1467=	XM_011542441.1:c.1467G>A	XM_011542441.1:c.1467G>T
TNFRSF8 transcript variant X4	XM_011542443.3:c.1137=	XM_011542443.3:c.1137G>A	XM_011542443.3:c.1137G>T
TNFRSF8 transcript variant X2	XM_011542443.2:c.1137=	XM_011542443.2:c.1137G>A	XM_011542443.2:c.1137G>T
TNFRSF8 transcript variant X3	XM_011542443.1:c.1137=	XM_011542443.1:c.1137G>A	XM_011542443.1:c.1137G>T
TNFRSF8 transcript variant 2	NM_152942.2:c.81=	NM_152942.2:c.81G>A	NM_152942.2:c.81G>T
TNFRSF8 transcript variant X2	XM_047434793.1:c.1416=	XM_047434793.1:c.1416G>A	XM_047434793.1:c.1416G>T
TNFRSF8 transcript variant X3	XM_047434799.1:c.1413=	XM_047434799.1:c.1413G>A	XM_047434799.1:c.1413G>T
TNFRSF8 transcript variant 2	NM_152942.1:c.81=	NM_152942.1:c.81G>A	NM_152942.1:c.81G>T
tumor necrosis factor receptor superfamily member 8 isoform 1 precursor	NP_001234.3:p.Pro490=	NP_001234.3:p.Pro490=	NP_001234.3:p.Pro490=
tumor necrosis factor receptor superfamily member 8 isoform 3	NP_001268359.2:p.Pro378=	NP_001268359.2:p.Pro378=	NP_001268359.2:p.Pro378=
tumor necrosis factor receptor superfamily member 8 isoform X1	XP_011540743.1:p.Pro489=	XP_011540743.1:p.Pro489=	XP_011540743.1:p.Pro489=
tumor necrosis factor receptor superfamily member 8 isoform X4	XP_011540745.1:p.Pro379=	XP_011540745.1:p.Pro379=	XP_011540745.1:p.Pro379=
tumor necrosis factor receptor superfamily member 8 isoform X2	XP_047290749.1:p.Pro472=	XP_047290749.1:p.Pro472=	XP_047290749.1:p.Pro472=
tumor necrosis factor receptor superfamily member 8 isoform X3	XP_047290755.1:p.Pro471=	XP_047290755.1:p.Pro471=	XP_047290755.1:p.Pro471=
tumor necrosis factor receptor superfamily member 8 isoform 1 precursor	NP_001234.2:p.Pro490=	NP_001234.2:p.Pro490=	NP_001234.2:p.Pro490=
tumor necrosis factor receptor superfamily member 8 isoform 3	NP_001268359.1:p.Pro378=	NP_001268359.1:p.Pro378=	NP_001268359.1:p.Pro378=

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#.

22 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss341933958	May 09, 2011 (134)
2	EVA_DECODE	ss1584221054	Apr 01, 2015 (144)
3	EVA_UK10K_ALSPAC	ss1599563022	Apr 01, 2015 (144)
4	EVA_UK10K_TWINSUK	ss1642557055	Apr 01, 2015 (144)
5	EVA_EXAC	ss1685309007	Apr 01, 2015 (144)
6	EVA_EXAC	ss1685309008	Apr 01, 2015 (144)
7	HUMAN_LONGEVITY	ss2160108749	Dec 20, 2016 (150)
8	GNOMAD	ss2731128616	Nov 08, 2017 (151)
9	GNOMAD	ss2746217954	Nov 08, 2017 (151)
10	GNOMAD	ss2751705093	Nov 08, 2017 (151)
11	SWEGEN	ss2986308079	Nov 08, 2017 (151)
12	EGCUT_WGS	ss3654408863	Jul 12, 2019 (153)
13	ACPOP	ss3726796708	Jul 12, 2019 (153)
14	EVA	ss3823561381	Apr 25, 2020 (154)
15	EVA	ss3825553774	Apr 25, 2020 (154)
16	KOGIC	ss3943841677	Apr 25, 2020 (154)
17	TOPMED	ss4439464897	Apr 25, 2021 (155)
18	TOPMED	ss4439464898	Apr 25, 2021 (155)
19	HUGCELL_USP	ss5442404669	Oct 12, 2022 (156)
20	EVA	ss5831550325	Oct 12, 2022 (156)
21	EVA	ss5848248356	Oct 12, 2022 (156)
22	EVA	ss5936766987	Oct 12, 2022 (156)
23	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 12198420	Oct 11, 2018 (152)
24	Genetic variation in the Estonian population	NC_000001.10 - 12198420	Oct 11, 2018 (152)
25	ExAC Submission ignored due to conflicting rows: Row 4488741 (NC_000001.10:12198419:G:G 116579/116678, NC_000001.10:12198419:G:T 99/116678) Row 4488742 (NC_000001.10:12198419:G:G 116676/116678, NC_000001.10:12198419:G:A 2/116678)	-	Oct 11, 2018 (152)
26	ExAC Submission ignored due to conflicting rows: Row 4488741 (NC_000001.10:12198419:G:G 116579/116678, NC_000001.10:12198419:G:T 99/116678) Row 4488742 (NC_000001.10:12198419:G:G 116676/116678, NC_000001.10:12198419:G:A 2/116678)	-	Oct 11, 2018 (152)
27	gnomAD - Genomes Submission ignored due to conflicting rows: Row 2706255 (NC_000001.11:12138362:G:A 1/140246) Row 2706256 (NC_000001.11:12138362:G:T 156/140246)	-	Apr 25, 2021 (155)
28	gnomAD - Genomes Submission ignored due to conflicting rows: Row 2706255 (NC_000001.11:12138362:G:A 1/140246) Row 2706256 (NC_000001.11:12138362:G:T 156/140246)	-	Apr 25, 2021 (155)
29	gnomAD - Exomes Submission ignored due to conflicting rows: Row 145252 (NC_000001.10:12198419:G:G 248694/248698, NC_000001.10:12198419:G:A 4/248698) Row 145253 (NC_000001.10:12198419:G:G 248507/248698, NC_000001.10:12198419:G:T 191/248698)	-	Jul 12, 2019 (153)
30	gnomAD - Exomes Submission ignored due to conflicting rows: Row 145252 (NC_000001.10:12198419:G:G 248694/248698, NC_000001.10:12198419:G:A 4/248698) Row 145253 (NC_000001.10:12198419:G:G 248507/248698, NC_000001.10:12198419:G:T 191/248698)	-	Jul 12, 2019 (153)
31	GO Exome Sequencing Project	NC_000001.10 - 12198420	Oct 11, 2018 (152)
32	Korean Genome Project	NC_000001.11 - 12138363	Apr 25, 2020 (154)
33	Northern Sweden	NC_000001.10 - 12198420	Jul 12, 2019 (153)
34	TopMed Submission ignored due to conflicting rows: Row 3071232 (NC_000001.11:12138362:G:A 1/264690) Row 3071233 (NC_000001.11:12138362:G:T 264/264690)	-	Apr 25, 2021 (155)
35	TopMed Submission ignored due to conflicting rows: Row 3071232 (NC_000001.11:12138362:G:A 1/264690) Row 3071233 (NC_000001.11:12138362:G:T 264/264690)	-	Apr 25, 2021 (155)
36	UK 10K study - Twins	NC_000001.10 - 12198420	Oct 11, 2018 (152)
37	ALFA	NC_000001.11 - 12138363	Apr 25, 2021 (155)
38	ClinVar	RCV000907629.3	Oct 12, 2022 (156)

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
ss1685309008, ss2731128616	NC_000001.10:12198419:G:A	NC_000001.11:12138362:G:A	(self)
219678, 5124173516, ss3943841677, ss4439464897	NC_000001.11:12138362:G:A	NC_000001.11:12138362:G:A	(self)
ss1584221054	NC_000001.9:12121006:G:T	NC_000001.11:12138362:G:T	(self)
203149, 147111, 20106, 81573, 203149, ss341933958, ss1599563022, ss1642557055, ss1685309007, ss2731128616, ss2746217954, ss2751705093, ss2986308079, ss3654408863, ss3726796708, ss3823561381, ss3825553774, ss5831550325, ss5848248356, ss5936766987	NC_000001.10:12198419:G:T	NC_000001.11:12138362:G:T	(self)
RCV000907629.3, 5124173516, ss2160108749, ss4439464898, ss5442404669	NC_000001.11:12138362:G:T	NC_000001.11:12138362:G:T	(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 rs142641214

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

rs142641214