Name: rs1491108453
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.

rs1491108453

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:55463946-55463949 (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: delCT
Variation Type: Indel Insertion and Deletion
Frequency: delCT=0.00047 (39/83328, GnomAD)
delCT=0.00008 (1/11862, ALFA)
delCT=0.005 (3/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TCF4 : Intron Variant
TCF4-AS1 : 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	11862	CTCT=0.99992	CT=0.00008	0.999831	0.000169	0
European	Sub	7618	CTCT=0.9999	CT=0.0001	0.999737	0.000263	0
African	Sub	2816	CTCT=1.0000	CT=0.0000	1.0	0.0	N/A
African Others	Sub	108	CTCT=1.000	CT=0.000	1.0	0.0	N/A
African American	Sub	2708	CTCT=1.0000	CT=0.0000	1.0	0.0	N/A
Asian	Sub	108	CTCT=1.000	CT=0.000	1.0	0.0	N/A
East Asian	Sub	84	CTCT=1.00	CT=0.00	1.0	0.0	N/A
Other Asian	Sub	24	CTCT=1.00	CT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CTCT=1.000	CT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CTCT=1.000	CT=0.000	1.0	0.0	N/A
South Asian	Sub	94	CTCT=1.00	CT=0.00	1.0	0.0	N/A
Other	Sub	470	CTCT=1.000	CT=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	83328	CTCT=0.99953	delCT=0.00047
gnomAD - Genomes	European	Sub	47364	CTCT=0.99924	delCT=0.00076
gnomAD - Genomes	African	Sub	24256	CTCT=0.99992	delCT=0.00008
gnomAD - Genomes	American	Sub	6842	CTCT=0.9999	delCT=0.0001
gnomAD - Genomes	Ashkenazi Jewish	Sub	2144	CTCT=1.0000	delCT=0.0000
gnomAD - Genomes	East Asian	Sub	1566	CTCT=1.0000	delCT=0.0000
gnomAD - Genomes	Other	Sub	1156	CTCT=1.0000	delCT=0.0000
Allele Frequency Aggregator	Total	Global	11862	CTCT=0.99992	delCT=0.00008
Allele Frequency Aggregator	European	Sub	7618	CTCT=0.9999	delCT=0.0001
Allele Frequency Aggregator	African	Sub	2816	CTCT=1.0000	delCT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	CTCT=1.000	delCT=0.000
Allele Frequency Aggregator	Other	Sub	470	CTCT=1.000	delCT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CTCT=1.000	delCT=0.000
Allele Frequency Aggregator	Asian	Sub	108	CTCT=1.000	delCT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	CTCT=1.00	delCT=0.00
Northern Sweden	ACPOP	Study-wide	600	CTCT=0.995	delCT=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 18	NC_000018.10:g.55463946CT[1]
GRCh37.p13 chr 18	NC_000018.9:g.53131177CT[1]
TCF4 RefSeqGene	NG_011716.2:g.177045AG[1]

Gene: TCF4, transcription factor 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TCF4 transcript variant 1	NM_001083962.2:c.207+129_… NM_001083962.2:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 3	NM_001243226.3:c.513+129_… NM_001243226.3:c.513+129_513+130del	N/A	Intron Variant
TCF4 transcript variant 4	NM_001243227.2:c.135+129_… NM_001243227.2:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 5	NM_001243228.2:c.207+129_… NM_001243228.2:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 6	NM_001243230.2:c.201+129_… NM_001243230.2:c.201+129_201+130del	N/A	Intron Variant
TCF4 transcript variant 7	NM_001243231.2:c.81+129_8… NM_001243231.2:c.81+129_81+130del	N/A	Intron Variant
TCF4 transcript variant 13	NM_001306207.1:c.135+129_… NM_001306207.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 15	NM_001330604.3:c.207+129_… NM_001330604.3:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 17	NM_001348211.2:c.81+129_8… NM_001348211.2:c.81+129_81+130del	N/A	Intron Variant
TCF4 transcript variant 23	NM_001348217.1:c.135+129_… NM_001348217.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 24	NM_001348218.2:c.135+129_… NM_001348218.2:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 25	NM_001348219.2:c.135+129_… NM_001348219.2:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 26	NM_001348220.1:c.135+129_… NM_001348220.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 27	NM_001369567.1:c.207+129_… NM_001369567.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 28	NM_001369568.1:c.207+129_… NM_001369568.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 29	NM_001369569.1:c.207+129_… NM_001369569.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 30	NM_001369570.1:c.207+129_… NM_001369570.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 31	NM_001369571.1:c.207+129_… NM_001369571.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 32	NM_001369572.1:c.207+129_… NM_001369572.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 33	NM_001369573.1:c.207+129_… NM_001369573.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 34	NM_001369574.1:c.207+129_… NM_001369574.1:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 35	NM_001369575.1:c.135+129_… NM_001369575.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 36	NM_001369576.1:c.135+129_… NM_001369576.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 37	NM_001369577.1:c.135+129_… NM_001369577.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 38	NM_001369578.1:c.135+129_… NM_001369578.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 39	NM_001369579.1:c.135+129_… NM_001369579.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 40	NM_001369580.1:c.135+129_… NM_001369580.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 41	NM_001369581.1:c.135+129_… NM_001369581.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 42	NM_001369582.1:c.135+129_… NM_001369582.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 43	NM_001369583.1:c.135+129_… NM_001369583.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 44	NM_001369584.1:c.135+129_… NM_001369584.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 45	NM_001369585.1:c.135+129_… NM_001369585.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 46	NM_001369586.1:c.135+129_… NM_001369586.1:c.135+129_135+130del	N/A	Intron Variant
TCF4 transcript variant 2	NM_003199.3:c.207+129_207… NM_003199.3:c.207+129_207+130del	N/A	Intron Variant
TCF4 transcript variant 8	NM_001243232.1:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 9	NM_001243233.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 10	NM_001243234.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 11	NM_001243235.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 12	NM_001243236.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 14	NM_001306208.1:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 16	NM_001330605.3:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 18	NM_001348212.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 19	NM_001348213.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 20	NM_001348214.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 21	NM_001348215.2:c.	N/A	Genic Upstream Transcript Variant
TCF4 transcript variant 22	NM_001348216.2:c.	N/A	Genic Upstream Transcript Variant

Gene: TCF4-AS1, TCF4 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TCF4-AS1 transcript	NR_132985.1:n.	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	CTCT=	delCT
GRCh38.p14 chr 18	NC_000018.10:g.55463946_55463949=	NC_000018.10:g.55463946CT[1]
GRCh37.p13 chr 18	NC_000018.9:g.53131177_53131180=	NC_000018.9:g.53131177CT[1]
TCF4 RefSeqGene	NG_011716.2:g.177045_177048=	NG_011716.2:g.177045AG[1]
TCF4 transcript variant 1	NM_001083962.1:c.207+130=	NM_001083962.1:c.207+129_207+130del
TCF4 transcript variant 1	NM_001083962.2:c.207+130=	NM_001083962.2:c.207+129_207+130del
TCF4 transcript variant 3	NM_001243226.1:c.513+130=	NM_001243226.1:c.513+129_513+130del
TCF4 transcript variant 3	NM_001243226.3:c.513+130=	NM_001243226.3:c.513+129_513+130del
TCF4 transcript variant 4	NM_001243227.1:c.135+130=	NM_001243227.1:c.135+129_135+130del
TCF4 transcript variant 4	NM_001243227.2:c.135+130=	NM_001243227.2:c.135+129_135+130del
TCF4 transcript variant 5	NM_001243228.1:c.207+130=	NM_001243228.1:c.207+129_207+130del
TCF4 transcript variant 5	NM_001243228.2:c.207+130=	NM_001243228.2:c.207+129_207+130del
TCF4 transcript variant 6	NM_001243230.1:c.201+130=	NM_001243230.1:c.201+129_201+130del
TCF4 transcript variant 6	NM_001243230.2:c.201+130=	NM_001243230.2:c.201+129_201+130del
TCF4 transcript variant 7	NM_001243231.1:c.81+130=	NM_001243231.1:c.81+129_81+130del
TCF4 transcript variant 7	NM_001243231.2:c.81+130=	NM_001243231.2:c.81+129_81+130del
TCF4 transcript variant 13	NM_001306207.1:c.135+130=	NM_001306207.1:c.135+129_135+130del
TCF4 transcript variant 15	NM_001330604.3:c.207+130=	NM_001330604.3:c.207+129_207+130del
TCF4 transcript variant 17	NM_001348211.2:c.81+130=	NM_001348211.2:c.81+129_81+130del
TCF4 transcript variant 23	NM_001348217.1:c.135+130=	NM_001348217.1:c.135+129_135+130del
TCF4 transcript variant 24	NM_001348218.2:c.135+130=	NM_001348218.2:c.135+129_135+130del
TCF4 transcript variant 25	NM_001348219.2:c.135+130=	NM_001348219.2:c.135+129_135+130del
TCF4 transcript variant 26	NM_001348220.1:c.135+130=	NM_001348220.1:c.135+129_135+130del
TCF4 transcript variant 27	NM_001369567.1:c.207+130=	NM_001369567.1:c.207+129_207+130del
TCF4 transcript variant 28	NM_001369568.1:c.207+130=	NM_001369568.1:c.207+129_207+130del
TCF4 transcript variant 29	NM_001369569.1:c.207+130=	NM_001369569.1:c.207+129_207+130del
TCF4 transcript variant 30	NM_001369570.1:c.207+130=	NM_001369570.1:c.207+129_207+130del
TCF4 transcript variant 31	NM_001369571.1:c.207+130=	NM_001369571.1:c.207+129_207+130del
TCF4 transcript variant 32	NM_001369572.1:c.207+130=	NM_001369572.1:c.207+129_207+130del
TCF4 transcript variant 33	NM_001369573.1:c.207+130=	NM_001369573.1:c.207+129_207+130del
TCF4 transcript variant 34	NM_001369574.1:c.207+130=	NM_001369574.1:c.207+129_207+130del
TCF4 transcript variant 35	NM_001369575.1:c.135+130=	NM_001369575.1:c.135+129_135+130del
TCF4 transcript variant 36	NM_001369576.1:c.135+130=	NM_001369576.1:c.135+129_135+130del
TCF4 transcript variant 37	NM_001369577.1:c.135+130=	NM_001369577.1:c.135+129_135+130del
TCF4 transcript variant 38	NM_001369578.1:c.135+130=	NM_001369578.1:c.135+129_135+130del
TCF4 transcript variant 39	NM_001369579.1:c.135+130=	NM_001369579.1:c.135+129_135+130del
TCF4 transcript variant 40	NM_001369580.1:c.135+130=	NM_001369580.1:c.135+129_135+130del
TCF4 transcript variant 41	NM_001369581.1:c.135+130=	NM_001369581.1:c.135+129_135+130del
TCF4 transcript variant 42	NM_001369582.1:c.135+130=	NM_001369582.1:c.135+129_135+130del
TCF4 transcript variant 43	NM_001369583.1:c.135+130=	NM_001369583.1:c.135+129_135+130del
TCF4 transcript variant 44	NM_001369584.1:c.135+130=	NM_001369584.1:c.135+129_135+130del
TCF4 transcript variant 45	NM_001369585.1:c.135+130=	NM_001369585.1:c.135+129_135+130del
TCF4 transcript variant 46	NM_001369586.1:c.135+130=	NM_001369586.1:c.135+129_135+130del
TCF4 transcript variant 2	NM_003199.2:c.207+130=	NM_003199.2:c.207+129_207+130del
TCF4 transcript variant 2	NM_003199.3:c.207+130=	NM_003199.3:c.207+129_207+130del
TCF4 transcript variant X1	XM_005266738.1:c.621+130=	XM_005266738.1:c.621+129_621+130del
TCF4 transcript variant X2	XM_005266739.1:c.477+130=	XM_005266739.1:c.477+129_477+130del
TCF4 transcript variant X3	XM_005266740.1:c.207+130=	XM_005266740.1:c.207+129_207+130del
TCF4 transcript variant X4	XM_005266741.1:c.207+130=	XM_005266741.1:c.207+129_207+130del
TCF4 transcript variant X5	XM_005266742.1:c.201+130=	XM_005266742.1:c.201+129_201+130del
TCF4 transcript variant X6	XM_005266743.1:c.135+130=	XM_005266743.1:c.135+129_135+130del
TCF4 transcript variant X7	XM_005266744.1:c.135+130=	XM_005266744.1:c.135+129_135+130del
TCF4 transcript variant X8	XM_005266745.1:c.135+130=	XM_005266745.1:c.135+129_135+130del
TCF4 transcript variant X9	XM_005266746.1:c.135+130=	XM_005266746.1:c.135+129_135+130del
TCF4 transcript variant X10	XM_005266747.1:c.81+130=	XM_005266747.1:c.81+129_81+130del
TCF4 transcript variant X11	XM_005266748.1:c.207+130=	XM_005266748.1:c.207+129_207+130del

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#.

3 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2957320499	Jan 10, 2018 (151)
2	EVA_DECODE	ss3701770340	Jul 13, 2019 (153)
3	ACPOP	ss3742592141	Jul 13, 2019 (153)
4	gnomAD - Genomes	NC_000018.10 - 55463946	Apr 27, 2021 (155)
5	Northern Sweden	NC_000018.9 - 53131177	Jul 13, 2019 (153)
6	ALFA	NC_000018.10 - 55463946	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
15877006, ss2957320499, ss3742592141	NC_000018.9:53131176:CT:	NC_000018.10:55463945:CTCT:CT	(self)
526165081, ss3701770340	NC_000018.10:55463945:CT:	NC_000018.10:55463945:CTCT:CT	(self)
12109015999	NC_000018.10:55463945:CTCT:CT	NC_000018.10:55463945:CTCT:CT	(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 rs1491108453

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

rs1491108453