Name: rs55649180
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.

rs55649180

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:5626004 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.015909 (4211/264690, TOPMED)
C=0.021912 (3074/140288, GnomAD)
C=0.02527 (485/19190, ALFA) (+ 12 more)
C=0.0095 (61/6404, 1000G_30x)
C=0.0092 (46/5008, 1000G)
C=0.0330 (148/4480, Estonian)
C=0.0257 (99/3854, ALSPAC)
C=0.0318 (118/3708, TWINSUK)
C=0.029 (29/998, GoNL)
C=0.040 (24/600, NorthernSweden)
C=0.03 (1/40, GENOME_DK)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TRIM34 : Intron Variant
TRIM5 : Intron Variant
TRIM6-TRIM34 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	19190	T=0.97473	C=0.02527
European	Sub	14286	T=0.96934	C=0.03066
African	Sub	2970	T=0.9939	C=0.0061
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2856	T=0.9937	C=0.0063
Asian	Sub	116	T=1.000	C=0.000
East Asian	Sub	88	T=1.00	C=0.00
Other Asian	Sub	28	T=1.00	C=0.00
Latin American 1	Sub	154	T=0.994	C=0.006
Latin American 2	Sub	616	T=0.995	C=0.005
South Asian	Sub	98	T=0.98	C=0.02
Other	Sub	950	T=0.976	C=0.024

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=0.984091	C=0.015909
gnomAD - Genomes	Global	Study-wide	140288	T=0.978088	C=0.021912
gnomAD - Genomes	European	Sub	75950	T=0.96621	C=0.03379
gnomAD - Genomes	African	Sub	42068	T=0.99451	C=0.00549
gnomAD - Genomes	American	Sub	13662	T=0.99041	C=0.00959
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9672	C=0.0328
gnomAD - Genomes	East Asian	Sub	3132	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9828	C=0.0172
Allele Frequency Aggregator	Total	Global	19190	T=0.97473	C=0.02527
Allele Frequency Aggregator	European	Sub	14286	T=0.96934	C=0.03066
Allele Frequency Aggregator	African	Sub	2970	T=0.9939	C=0.0061
Allele Frequency Aggregator	Other	Sub	950	T=0.976	C=0.024
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.995	C=0.005
Allele Frequency Aggregator	Latin American 1	Sub	154	T=0.994	C=0.006
Allele Frequency Aggregator	Asian	Sub	116	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.98	C=0.02
1000Genomes_30x	Global	Study-wide	6404	T=0.9905	C=0.0095
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9660	C=0.0340
1000Genomes_30x	South Asian	Sub	1202	T=0.9967	C=0.0033
1000Genomes_30x	East Asian	Sub	1170	T=0.9983	C=0.0017
1000Genomes_30x	American	Sub	980	T=0.988	C=0.012
1000Genomes	Global	Study-wide	5008	T=0.9908	C=0.0092
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.9652	C=0.0348
1000Genomes	South Asian	Sub	978	T=0.997	C=0.003
1000Genomes	American	Sub	694	T=0.990	C=0.010
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9670	C=0.0330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9743	C=0.0257
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9682	C=0.0318
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.971	C=0.029
Northern Sweden	ACPOP	Study-wide	600	T=0.960	C=0.040
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
SGDP_PRJ	Global	Study-wide	6	T=0.5	C=0.5
Siberian	Global	Study-wide	2	T=0.5	C=0.5

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 11	NC_000011.10:g.5626004T>C
GRCh37.p13 chr 11	NC_000011.9:g.5647234T>C

Gene: TRIM6-TRIM34, TRIM6-TRIM34 readthrough (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRIM6-TRIM34 transcript	NM_001003819.4:c.986-6251… NM_001003819.4:c.986-6251T>C	N/A	Intron Variant

Gene: TRIM34, tripartite motif containing 34 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRIM34 transcript variant 4	NM_001003827.1:c.-78+5981… NM_001003827.1:c.-78+5981T>C	N/A	Intron Variant
TRIM34 transcript variant 1	NM_021616.6:c.-78+944T>C	N/A	Intron Variant
TRIM34 transcript variant 3	NM_130390.2:c.	N/A	Genic Upstream Transcript Variant

Gene: TRIM5, tripartite motif containing 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRIM5 transcript variant alpha	NM_033034.3:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant gamma	NM_033092.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant delta	NM_033093.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X1	XM_005253183.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X2	XM_005253184.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X11	XM_006718358.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X4	XM_011520426.4:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X3	XM_017018460.3:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X5	XM_017018461.3:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X12	XM_017018463.3:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X8	XM_047427783.1:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X12	XM_047427784.1:c.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X6	XR_001748014.3:n.	N/A	Intron Variant
TRIM5 transcript variant X9	XR_007062518.1:n.	N/A	Intron Variant
TRIM5 transcript variant X10	XR_007062519.1:n.	N/A	Intron Variant
TRIM5 transcript variant X15	XR_007062522.1:n.	N/A	Intron Variant
TRIM5 transcript variant X7	XR_007062517.1:n.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X13	XR_007062520.1:n.	N/A	Genic Downstream Transcript Variant
TRIM5 transcript variant X14	XR_007062521.1:n.	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	T=	C
GRCh38.p14 chr 11	NC_000011.10:g.5626004=	NC_000011.10:g.5626004T>C
GRCh37.p13 chr 11	NC_000011.9:g.5647234=	NC_000011.9:g.5647234T>C
TRIM6-TRIM34 transcript	NM_001003819.3:c.986-6251=	NM_001003819.3:c.986-6251T>C
TRIM6-TRIM34 transcript	NM_001003819.4:c.986-6251=	NM_001003819.4:c.986-6251T>C
TRIM34 transcript variant 4	NM_001003827.1:c.-78+5981=	NM_001003827.1:c.-78+5981T>C
TRIM34 transcript variant 1	NM_021616.5:c.-78+944=	NM_021616.5:c.-78+944T>C
TRIM34 transcript variant 1	NM_021616.6:c.-78+944=	NM_021616.6:c.-78+944T>C
TRIM34 transcript variant X1	XM_005252986.1:c.-128-534=	XM_005252986.1:c.-128-534T>C

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#.

32 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77380646	Dec 06, 2007 (129)
2	1000GENOMES	ss235428192	Jul 15, 2010 (132)
3	ILLUMINA	ss533310503	Sep 08, 2015 (146)
4	EVA-GONL	ss988163512	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1077468179	Aug 21, 2014 (142)
6	1000GENOMES	ss1339954159	Aug 21, 2014 (142)
7	EVA_GENOME_DK	ss1575494926	Apr 01, 2015 (144)
8	EVA_DECODE	ss1597839924	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1625903224	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1668897257	Apr 01, 2015 (144)
11	JJLAB	ss2026504385	Sep 14, 2016 (149)
12	USC_VALOUEV	ss2154791246	Dec 20, 2016 (150)
13	HUMAN_LONGEVITY	ss2179856111	Dec 20, 2016 (150)
14	GNOMAD	ss2895878577	Nov 08, 2017 (151)
15	SWEGEN	ss3007529597	Nov 08, 2017 (151)
16	CSHL	ss3349432402	Nov 08, 2017 (151)
17	ILLUMINA	ss3626589361	Oct 12, 2018 (152)
18	EGCUT_WGS	ss3674925726	Jul 13, 2019 (153)
19	EVA_DECODE	ss3691134272	Jul 13, 2019 (153)
20	ACPOP	ss3737882791	Jul 13, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3814240847	Jul 13, 2019 (153)
22	SGDP_PRJ	ss3875561080	Apr 26, 2020 (154)
23	TOPMED	ss4873807484	Apr 26, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5286263681	Oct 16, 2022 (156)
25	EVA	ss5397484695	Oct 16, 2022 (156)
26	HUGCELL_USP	ss5481581307	Oct 16, 2022 (156)
27	EVA	ss5510236936	Oct 16, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5581313901	Oct 16, 2022 (156)
29	SANFORD_IMAGENETICS	ss5650555710	Oct 16, 2022 (156)
30	EVA	ss5836206081	Oct 16, 2022 (156)
31	EVA	ss5918666719	Oct 16, 2022 (156)
32	EVA	ss5941858170	Oct 16, 2022 (156)
33	1000Genomes	NC_000011.9 - 5647234	Oct 12, 2018 (152)
34	1000Genomes_30x	NC_000011.10 - 5626004	Oct 16, 2022 (156)
35	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 5647234	Oct 12, 2018 (152)
36	Genetic variation in the Estonian population	NC_000011.9 - 5647234	Oct 12, 2018 (152)
37	The Danish reference pan genome	NC_000011.9 - 5647234	Apr 26, 2020 (154)
38	gnomAD - Genomes	NC_000011.10 - 5626004	Apr 26, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000011.9 - 5647234	Apr 26, 2020 (154)
40	Northern Sweden	NC_000011.9 - 5647234	Jul 13, 2019 (153)
41	SGDP_PRJ	NC_000011.9 - 5647234	Apr 26, 2020 (154)
42	Siberian	NC_000011.9 - 5647234	Apr 26, 2020 (154)
43	TopMed	NC_000011.10 - 5626004	Apr 26, 2021 (155)
44	UK 10K study - Twins	NC_000011.9 - 5647234	Oct 12, 2018 (152)
45	ALFA	NC_000011.10 - 5626004	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
ss77380646, ss1597839924	NC_000011.8:5603809:T:C	NC_000011.10:5626003:T:C	(self)
52431286, 29121493, 20663974, 2423813, 12983599, 11167656, 27578060, 7307600, 29121493, ss235428192, ss533310503, ss988163512, ss1077468179, ss1339954159, ss1575494926, ss1625903224, ss1668897257, ss2026504385, ss2154791246, ss2895878577, ss3007529597, ss3349432402, ss3626589361, ss3674925726, ss3737882791, ss3875561080, ss5397484695, ss5510236936, ss5650555710, ss5836206081, ss5941858170	NC_000011.9:5647233:T:C	NC_000011.10:5626003:T:C	(self)
68839836, 370208441, 89353140, 14749182589, ss2179856111, ss3691134272, ss3814240847, ss4873807484, ss5286263681, ss5481581307, ss5581313901, ss5918666719	NC_000011.10:5626003:T:C	NC_000011.10:5626003:T:C	(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 rs55649180

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
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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

rs55649180