Name: rs1491376457
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.

rs1491376457

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:93809774-93809776 (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: delTA
Variation Type: Indel Insertion and Deletion
Frequency: delTA=0.07452 (3220/43210, GnomAD)
delTA=0.00050 (14/27948, 14KJPN)
delTA=0.00075 (12/16078, 8.3KJPN) (+ 2 more)
delTA=0.01824 (293/16067, ALFA)
delTA=0.0345 (62/1798, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BCAR3 : 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	16067	ATA=0.98176	A=0.01824	0.963541	0.036459	2
European	Sub	11815	ATA=0.98942	A=0.01058	0.978922	0.021078	0
African	Sub	2816	ATA=0.9471	A=0.0529	0.894176	0.105824	3
African Others	Sub	108	ATA=0.981	A=0.019	0.962963	0.037037	0
African American	Sub	2708	ATA=0.9457	A=0.0543	0.891433	0.108567	3
Asian	Sub	108	ATA=0.991	A=0.009	0.981481	0.018519	0
East Asian	Sub	84	ATA=1.00	A=0.00	1.0	0.0	N/A
Other Asian	Sub	24	ATA=0.96	A=0.04	0.916667	0.083333	0
Latin American 1	Sub	146	ATA=0.979	A=0.021	0.958904	0.041096	0
Latin American 2	Sub	610	ATA=0.993	A=0.007	0.986885	0.013115	0
South Asian	Sub	94	ATA=1.00	A=0.00	1.0	0.0	N/A
Other	Sub	478	ATA=0.977	A=0.023	0.953975	0.046025	0

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	43210	ATA=0.92548	delTA=0.07452
gnomAD - Genomes	European	Sub	24374	ATA=0.96537	delTA=0.03463
gnomAD - Genomes	African	Sub	12382	ATA=0.83314	delTA=0.16686
gnomAD - Genomes	American	Sub	3816	ATA=0.9604	delTA=0.0396
gnomAD - Genomes	Ashkenazi Jewish	Sub	1204	ATA=0.9095	delTA=0.0905
gnomAD - Genomes	East Asian	Sub	796	ATA=0.997	delTA=0.003
gnomAD - Genomes	Other	Sub	638	ATA=0.925	delTA=0.075
14KJPN	JAPANESE	Study-wide	27948	ATA=0.99950	delTA=0.00050
8.3KJPN	JAPANESE	Study-wide	16078	ATA=0.99925	delTA=0.00075
Allele Frequency Aggregator	Total	Global	16067	ATA=0.98176	delTA=0.01824
Allele Frequency Aggregator	European	Sub	11815	ATA=0.98942	delTA=0.01058
Allele Frequency Aggregator	African	Sub	2816	ATA=0.9471	delTA=0.0529
Allele Frequency Aggregator	Latin American 2	Sub	610	ATA=0.993	delTA=0.007
Allele Frequency Aggregator	Other	Sub	478	ATA=0.977	delTA=0.023
Allele Frequency Aggregator	Latin American 1	Sub	146	ATA=0.979	delTA=0.021
Allele Frequency Aggregator	Asian	Sub	108	ATA=0.991	delTA=0.009
Allele Frequency Aggregator	South Asian	Sub	94	ATA=1.00	delTA=0.00
Korean Genome Project	KOREAN	Study-wide	1798	ATA=0.9655	delTA=0.0345

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.93809775_93809776del
GRCh37.p13 chr 1	NC_000001.10:g.94275331_94275332del

Gene: BCAR3, BCAR3 adaptor protein, NSP family member (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BCAR3 transcript variant 1	NM_001261408.2:c.-63+3579… NM_001261408.2:c.-63+35792_-63+35793del	N/A	Intron Variant
BCAR3 transcript variant 3	NM_001261409.1:c.	N/A	Genic Upstream Transcript Variant
BCAR3 transcript variant 4	NM_001261410.2:c.	N/A	Genic Upstream Transcript Variant
BCAR3 transcript variant 5	NM_001308251.1:c.	N/A	Genic Upstream Transcript Variant
BCAR3 transcript variant 2	NM_003567.4:c.	N/A	Genic Upstream Transcript Variant
BCAR3 transcript variant 6	NR_171551.1: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	ATA=	delTA
GRCh38.p14 chr 1	NC_000001.11:g.93809774_93809776=	NC_000001.11:g.93809775_93809776del
GRCh37.p13 chr 1	NC_000001.10:g.94275330_94275332=	NC_000001.10:g.94275331_94275332del
BCAR3 transcript variant 1	NM_001261408.1:c.-63+35793=	NM_001261408.1:c.-63+35792_-63+35793del
BCAR3 transcript variant 1	NM_001261408.2:c.-63+35793=	NM_001261408.2:c.-63+35792_-63+35793del

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#.

8 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SWEGEN	ss2987242484	Jan 10, 2018 (151)
2	EVA_DECODE	ss3687290034	Jul 12, 2019 (153)
3	KOGIC	ss3945017737	Apr 25, 2020 (154)
4	GNOMAD	ss3998291810	Apr 25, 2021 (155)
5	TOMMO_GENOMICS	ss5145136362	Apr 25, 2021 (155)
6	HUGCELL_USP	ss5444152129	Oct 12, 2022 (156)
7	TOMMO_GENOMICS	ss5670246254	Oct 12, 2022 (156)
8	YY_MCH	ss5800826441	Oct 12, 2022 (156)
9	gnomAD - Genomes	NC_000001.11 - 93809774	Apr 25, 2021 (155)
10	Korean Genome Project	NC_000001.11 - 93809774	Apr 25, 2020 (154)
11	8.3KJPN	NC_000001.10 - 94275330	Apr 25, 2021 (155)
12	14KJPN	NC_000001.11 - 93809774	Oct 12, 2022 (156)
13	ALFA	NC_000001.11 - 93809774	Apr 25, 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
3105669, ss2987242484, ss5145136362	NC_000001.10:94275329:AT:	NC_000001.11:93809773:ATA:A	(self)
19126342, 1395738, 4083358, ss3687290034, ss3945017737, ss3998291810, ss5444152129, ss5670246254, ss5800826441	NC_000001.11:93809773:AT:	NC_000001.11:93809773:ATA:A	(self)
2610655454	NC_000001.11:93809773:ATA:A	NC_000001.11:93809773:ATA: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 rs1491376457

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

rs1491376457