Name: rs1491569769
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.

rs1491569769

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:2975182-2975184 (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: delCA
Variation Type: Indel Insertion and Deletion
Frequency: delCA=0.068397 (9405/137506, GnomAD)
delCA=0.00340 (96/28258, 14KJPN)
delCA=0.00292 (49/16760, 8.3KJPN) (+ 2 more)
delCA=0.0429 (275/6404, 1000G_30x)
delCA=0.1014 (450/4440, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TEAD4 : 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	4440	ACA=0.8986	A=0.1014	0.835135	0.037838	0.127027	32
European	Sub	4432	ACA=0.8985	A=0.1015	0.834838	0.037906	0.127256	32
African	Sub	0	ACA=0	A=0	0	0	0	N/A
African Others	Sub	0	ACA=0	A=0	0	0	0	N/A
African American	Sub	0	ACA=0	A=0	0	0	0	N/A
Asian	Sub	0	ACA=0	A=0	0	0	0	N/A
East Asian	Sub	0	ACA=0	A=0	0	0	0	N/A
Other Asian	Sub	0	ACA=0	A=0	0	0	0	N/A
Latin American 1	Sub	0	ACA=0	A=0	0	0	0	N/A
Latin American 2	Sub	0	ACA=0	A=0	0	0	0	N/A
South Asian	Sub	0	ACA=0	A=0	0	0	0	N/A
Other	Sub	8	ACA=1.0	A=0.0	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
gnomAD - Genomes	Global	Study-wide	137506	ACA=0.931603	delCA=0.068397
gnomAD - Genomes	European	Sub	74154	ACA=0.90807	delCA=0.09193
gnomAD - Genomes	African	Sub	41514	ACA=0.97904	delCA=0.02096
gnomAD - Genomes	American	Sub	13324	ACA=0.89920	delCA=0.10080
gnomAD - Genomes	Ashkenazi Jewish	Sub	3304	ACA=0.9410	delCA=0.0590
gnomAD - Genomes	East Asian	Sub	3112	ACA=0.9971	delCA=0.0029
gnomAD - Genomes	Other	Sub	2098	ACA=0.9185	delCA=0.0815
14KJPN	JAPANESE	Study-wide	28258	ACA=0.99660	delCA=0.00340
8.3KJPN	JAPANESE	Study-wide	16760	ACA=0.99708	delCA=0.00292
1000Genomes_30x	Global	Study-wide	6404	ACA=0.9571	delCA=0.0429
1000Genomes_30x	African	Sub	1786	ACA=0.9916	delCA=0.0084
1000Genomes_30x	Europe	Sub	1266	ACA=0.9100	delCA=0.0900
1000Genomes_30x	South Asian	Sub	1202	ACA=0.9401	delCA=0.0599
1000Genomes_30x	East Asian	Sub	1170	ACA=0.9983	delCA=0.0017
1000Genomes_30x	American	Sub	980	ACA=0.927	delCA=0.073
Allele Frequency Aggregator	Total	Global	4440	ACA=0.8986	delCA=0.1014
Allele Frequency Aggregator	European	Sub	4432	ACA=0.8985	delCA=0.1015
Allele Frequency Aggregator	Other	Sub	8	ACA=1.0	delCA=0.0
Allele Frequency Aggregator	Latin American 1	Sub	0	ACA=0	delCA=0
Allele Frequency Aggregator	Latin American 2	Sub	0	ACA=0	delCA=0
Allele Frequency Aggregator	South Asian	Sub	0	ACA=0	delCA=0
Allele Frequency Aggregator	African	Sub	0	ACA=0	delCA=0
Allele Frequency Aggregator	Asian	Sub	0	ACA=0	delCA=0

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 12	NC_000012.12:g.2975183_2975184del
GRCh37.p13 chr 12	NC_000012.11:g.3084349_3084350del
TEAD4 RefSeqGene	NG_029958.1:g.20872_20873del

Gene: TEAD4, TEA domain transcription factor 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TEAD4 transcript variant 1	NM_003213.4:c.-30+15143_-… NM_003213.4:c.-30+15143_-30+15144del	N/A	Intron Variant
TEAD4 transcript variant 2	NM_201441.3:c.-30+15143_-… NM_201441.3:c.-30+15143_-30+15144del	N/A	Intron Variant
TEAD4 transcript variant 3	NM_201443.3:c.-162+15143_… NM_201443.3:c.-162+15143_-162+15144del	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	ACA=	delCA
GRCh38.p14 chr 12	NC_000012.12:g.2975182_2975184=	NC_000012.12:g.2975183_2975184del
GRCh37.p13 chr 12	NC_000012.11:g.3084348_3084350=	NC_000012.11:g.3084349_3084350del
TEAD4 RefSeqGene	NG_029958.1:g.20871_20873=	NG_029958.1:g.20872_20873del
TEAD4 transcript variant 1	NM_003213.3:c.-30+15142=	NM_003213.3:c.-30+15143_-30+15144del
TEAD4 transcript variant 1	NM_003213.4:c.-30+15142=	NM_003213.4:c.-30+15143_-30+15144del
TEAD4 transcript variant 2	NM_201441.2:c.-30+15142=	NM_201441.2:c.-30+15143_-30+15144del
TEAD4 transcript variant 2	NM_201441.3:c.-30+15142=	NM_201441.3:c.-30+15143_-30+15144del
TEAD4 transcript variant 3	NM_201443.2:c.-162+15142=	NM_201443.2:c.-162+15143_-162+15144del
TEAD4 transcript variant 3	NM_201443.3:c.-162+15142=	NM_201443.3:c.-162+15143_-162+15144del
TEAD4 transcript variant X1	XM_005253755.1:c.52+14829=	XM_005253755.1:c.52+14830_52+14831del
TEAD4 transcript variant X2	XM_005253756.1:c.52+14829=	XM_005253756.1:c.52+14830_52+14831del
TEAD4 transcript variant X3	XM_005253757.1:c.-249+14986=	XM_005253757.1:c.-249+14987_-249+14988del

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#.

10 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_DECODE	ss1598844554	Jan 10, 2018 (151)
2	GNOMAD	ss2906662802	Jan 10, 2018 (151)
3	SWEGEN	ss3009100980	Jan 10, 2018 (151)
4	EVA_DECODE	ss3692991042	Jul 13, 2019 (153)
5	TOMMO_GENOMICS	ss5204783439	Apr 27, 2021 (155)
6	1000G_HIGH_COVERAGE	ss5289591974	Oct 17, 2022 (156)
7	HUGCELL_USP	ss5484508050	Oct 17, 2022 (156)
8	1000G_HIGH_COVERAGE	ss5586414942	Oct 17, 2022 (156)
9	SANFORD_IMAGENETICS	ss5652466425	Oct 17, 2022 (156)
10	TOMMO_GENOMICS	ss5753492651	Oct 17, 2022 (156)
11	1000Genomes_30x	NC_000012.12 - 2975182	Oct 17, 2022 (156)
12	gnomAD - Genomes	NC_000012.12 - 2975182	Apr 27, 2021 (155)
13	8.3KJPN	NC_000012.11 - 3084348	Apr 27, 2021 (155)
14	14KJPN	NC_000012.12 - 2975182	Oct 17, 2022 (156)
15	ALFA	NC_000012.12 - 2975182	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
ss1598844554	NC_000012.10:2954608:AC:	NC_000012.12:2975181:ACA:A	(self)
62752746, ss2906662802, ss3009100980, ss5204783439, ss5652466425	NC_000012.11:3084347:AC:	NC_000012.12:2975181:ACA:A	(self)
73940877, 397564556, 87329755, ss3692991042, ss5289591974, ss5484508050, ss5586414942, ss5753492651	NC_000012.12:2975181:AC:	NC_000012.12:2975181:ACA:A	(self)
7542433916	NC_000012.12:2975181:ACA:A	NC_000012.12:2975181:ACA:A	(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 rs1491569769

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

rs1491569769