Name: rs1262566140
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.

rs1262566140

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:27657279-27657284 (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: delC / dupC / dupCC
Variation Type: Indel Insertion and Deletion
Frequency: dupC=0.00005 (1/18520, ALFA)
delC=0.0002 (1/6404, 1000G_30x)
dupC=0.0002 (1/4480, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BDNF-AS : Intron Variant
BDNF : 3 Prime UTR 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	18520	CCCCCC=0.99995	CCCCC=0.00000, CCCCCCC=0.00005, CCCCCCCC=0.00000	0.999892	0.000108	0
European	Sub	14152	CCCCCC=0.99993	CCCCC=0.00000, CCCCCCC=0.00007, CCCCCCCC=0.00000	0.999859	0.000141	0
African	Sub	2898	CCCCCC=1.0000	CCCCC=0.0000, CCCCCCC=0.0000, CCCCCCCC=0.0000	1.0	0.0	N/A
African Others	Sub	114	CCCCCC=1.000	CCCCC=0.000, CCCCCCC=0.000, CCCCCCCC=0.000	1.0	0.0	N/A
African American	Sub	2784	CCCCCC=1.0000	CCCCC=0.0000, CCCCCCC=0.0000, CCCCCCCC=0.0000	1.0	0.0	N/A
Asian	Sub	112	CCCCCC=1.000	CCCCC=0.000, CCCCCCC=0.000, CCCCCCCC=0.000	1.0	0.0	N/A
East Asian	Sub	86	CCCCCC=1.00	CCCCC=0.00, CCCCCCC=0.00, CCCCCCCC=0.00	1.0	0.0	N/A
Other Asian	Sub	26	CCCCCC=1.00	CCCCC=0.00, CCCCCCC=0.00, CCCCCCCC=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CCCCCC=1.000	CCCCC=0.000, CCCCCCC=0.000, CCCCCCCC=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CCCCCC=1.000	CCCCC=0.000, CCCCCCC=0.000, CCCCCCCC=0.000	1.0	0.0	N/A
South Asian	Sub	98	CCCCCC=1.00	CCCCC=0.00, CCCCCCC=0.00, CCCCCCCC=0.00	1.0	0.0	N/A
Other	Sub	504	CCCCCC=1.000	CCCCC=0.000, CCCCCCC=0.000, CCCCCCCC=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
Allele Frequency Aggregator	Total	Global	18520	(C)₆=0.99995	delC=0.00000, dupC=0.00005, dupCC=0.00000
Allele Frequency Aggregator	European	Sub	14152	(C)₆=0.99993	delC=0.00000, dupC=0.00007, dupCC=0.00000
Allele Frequency Aggregator	African	Sub	2898	(C)₆=1.0000	delC=0.0000, dupC=0.0000, dupCC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(C)₆=1.000	delC=0.000, dupC=0.000, dupCC=0.000
Allele Frequency Aggregator	Other	Sub	504	(C)₆=1.000	delC=0.000, dupC=0.000, dupCC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(C)₆=1.000	delC=0.000, dupC=0.000, dupCC=0.000
Allele Frequency Aggregator	Asian	Sub	112	(C)₆=1.000	delC=0.000, dupC=0.000, dupCC=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(C)₆=1.00	delC=0.00, dupC=0.00, dupCC=0.00
1000Genomes_30x	Global	Study-wide	6404	(C)₆=0.9998	delC=0.0002
1000Genomes_30x	African	Sub	1786	(C)₆=1.0000	delC=0.0000
1000Genomes_30x	Europe	Sub	1266	(C)₆=0.9992	delC=0.0008
1000Genomes_30x	South Asian	Sub	1202	(C)₆=1.0000	delC=0.0000
1000Genomes_30x	East Asian	Sub	1170	(C)₆=1.0000	delC=0.0000
1000Genomes_30x	American	Sub	980	(C)₆=1.000	delC=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupC=0.0002

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.27657284del
GRCh38.p14 chr 11	NC_000011.10:g.27657284dup
GRCh38.p14 chr 11	NC_000011.10:g.27657283_27657284dup
GRCh37.p13 chr 11	NC_000011.9:g.27678831del
GRCh37.p13 chr 11	NC_000011.9:g.27678831dup
GRCh37.p13 chr 11	NC_000011.9:g.27678830_27678831dup
BDNF RefSeqGene	NG_011794.1:g.69779del
BDNF RefSeqGene	NG_011794.1:g.69779dup
BDNF RefSeqGene	NG_011794.1:g.69778_69779dup

Gene: BDNF, brain derived neurotrophic factor (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BDNF transcript variant 2	NM_170732.4:c.536_541=	N/A	3 Prime UTR Variant
BDNF transcript variant 7	NM_001143805.1:c.536_54… NM_001143805.1:c.536_541=	N/A	3 Prime UTR Variant
BDNF transcript variant 8	NM_001143806.1:c.536_54… NM_001143806.1:c.536_541=	N/A	3 Prime UTR Variant
BDNF transcript variant 4	NM_001709.5:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 13	NM_001143813.2:c.537_54… NM_001143813.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 3	NM_170731.5:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 9	NM_001143807.2:c.537_54… NM_001143807.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 14	NM_001143814.2:c.537_54… NM_001143814.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 10	NM_001143808.2:c.537_54… NM_001143808.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 1	NM_170735.6:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 16	NM_001143816.2:c.537_54… NM_001143816.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 5	NM_170733.4:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 11	NM_001143811.2:c.537_54… NM_001143811.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 12	NM_001143812.2:c.537_54… NM_001143812.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 17	NM_001143809.2:c.537_54… NM_001143809.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 18	NM_001143810.2:c.537_54… NM_001143810.2:c.537_542=	N/A	3 Prime UTR Variant
BDNF transcript variant 6	NM_170734.4:c.537_542=	N/A	3 Prime UTR Variant

Gene: BDNF-AS, BDNF antisense RNA (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BDNF-AS transcript variant BT2B	NR_002832.2:n.	N/A	Intron Variant
BDNF-AS transcript variant BT1C	NR_033312.1:n.	N/A	Intron Variant
BDNF-AS transcript variant BT1A	NR_033313.1:n.	N/A	Intron Variant
BDNF-AS transcript variant BT2A	NR_033314.1:n.	N/A	Intron Variant
BDNF-AS transcript variant BT1B	NR_033315.1: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	(C)₆=	delC	dupC	dupCC
GRCh38.p14 chr 11	NC_000011.10:g.27657279_27657284=	NC_000011.10:g.27657284del	NC_000011.10:g.27657284dup	NC_000011.10:g.27657283_27657284dup
GRCh37.p13 chr 11	NC_000011.9:g.27678826_27678831=	NC_000011.9:g.27678831del	NC_000011.9:g.27678831dup	NC_000011.9:g.27678830_27678831dup
BDNF RefSeqGene	NG_011794.1:g.69774_69779=	NG_011794.1:g.69779del	NG_011794.1:g.69779dup	NG_011794.1:g.69778_69779dup
BDNF transcript variant 1	NM_170735.6:c.537_542=	NM_170735.6:c.*542del	NM_170735.6:c.*542dup	NM_170735.6:c.541_542dup
BDNF transcript variant 1	NM_170735.5:c.536_541=	NM_170735.5:c.*541del	NM_170735.5:c.*541dup	NM_170735.5:c.540_541dup
BDNF transcript variant 3	NM_170731.5:c.537_542=	NM_170731.5:c.*542del	NM_170731.5:c.*542dup	NM_170731.5:c.541_542dup
BDNF transcript variant 3	NM_170731.4:c.536_541=	NM_170731.4:c.*541del	NM_170731.4:c.*541dup	NM_170731.4:c.540_541dup
BDNF transcript variant 4	NM_001709.5:c.537_542=	NM_001709.5:c.*542del	NM_001709.5:c.*542dup	NM_001709.5:c.541_542dup
BDNF transcript variant 4	NM_001709.4:c.536_541=	NM_001709.4:c.*541del	NM_001709.4:c.*541dup	NM_001709.4:c.540_541dup
BDNF transcript variant 2	NM_170732.4:c.536_541=	NM_170732.4:c.*541del	NM_170732.4:c.*541dup	NM_170732.4:c.540_541dup
BDNF transcript variant 5	NM_170733.4:c.537_542=	NM_170733.4:c.*542del	NM_170733.4:c.*542dup	NM_170733.4:c.541_542dup
BDNF transcript variant 5	NM_170733.3:c.536_541=	NM_170733.3:c.*541del	NM_170733.3:c.*541dup	NM_170733.3:c.540_541dup
BDNF transcript variant 6	NM_170734.4:c.537_542=	NM_170734.4:c.*542del	NM_170734.4:c.*542dup	NM_170734.4:c.541_542dup
BDNF transcript variant 6	NM_170734.3:c.536_541=	NM_170734.3:c.*541del	NM_170734.3:c.*541dup	NM_170734.3:c.540_541dup
BDNF transcript variant 16	NM_001143816.2:c.537_542=	NM_001143816.2:c.*542del	NM_001143816.2:c.*542dup	NM_001143816.2:c.541_542dup
BDNF transcript variant 16	NM_001143816.1:c.536_541=	NM_001143816.1:c.*541del	NM_001143816.1:c.*541dup	NM_001143816.1:c.540_541dup
BDNF transcript variant 11	NM_001143811.2:c.537_542=	NM_001143811.2:c.*542del	NM_001143811.2:c.*542dup	NM_001143811.2:c.541_542dup
BDNF transcript variant 11	NM_001143811.1:c.536_541=	NM_001143811.1:c.*541del	NM_001143811.1:c.*541dup	NM_001143811.1:c.540_541dup
BDNF transcript variant 14	NM_001143814.2:c.537_542=	NM_001143814.2:c.*542del	NM_001143814.2:c.*542dup	NM_001143814.2:c.541_542dup
BDNF transcript variant 14	NM_001143814.1:c.536_541=	NM_001143814.1:c.*541del	NM_001143814.1:c.*541dup	NM_001143814.1:c.540_541dup
BDNF transcript variant 18	NM_001143810.2:c.537_542=	NM_001143810.2:c.*542del	NM_001143810.2:c.*542dup	NM_001143810.2:c.541_542dup
BDNF transcript variant 18	NM_001143810.1:c.536_541=	NM_001143810.1:c.*541del	NM_001143810.1:c.*541dup	NM_001143810.1:c.540_541dup
BDNF transcript variant 13	NM_001143813.2:c.537_542=	NM_001143813.2:c.*542del	NM_001143813.2:c.*542dup	NM_001143813.2:c.541_542dup
BDNF transcript variant 13	NM_001143813.1:c.536_541=	NM_001143813.1:c.*541del	NM_001143813.1:c.*541dup	NM_001143813.1:c.540_541dup
BDNF transcript variant 12	NM_001143812.2:c.537_542=	NM_001143812.2:c.*542del	NM_001143812.2:c.*542dup	NM_001143812.2:c.541_542dup
BDNF transcript variant 12	NM_001143812.1:c.536_541=	NM_001143812.1:c.*541del	NM_001143812.1:c.*541dup	NM_001143812.1:c.540_541dup
BDNF transcript variant 17	NM_001143809.2:c.537_542=	NM_001143809.2:c.*542del	NM_001143809.2:c.*542dup	NM_001143809.2:c.541_542dup
BDNF transcript variant 17	NM_001143809.1:c.536_541=	NM_001143809.1:c.*541del	NM_001143809.1:c.*541dup	NM_001143809.1:c.540_541dup
BDNF transcript variant 10	NM_001143808.2:c.537_542=	NM_001143808.2:c.*542del	NM_001143808.2:c.*542dup	NM_001143808.2:c.541_542dup
BDNF transcript variant 10	NM_001143808.1:c.536_541=	NM_001143808.1:c.*541del	NM_001143808.1:c.*541dup	NM_001143808.1:c.540_541dup
BDNF transcript variant 9	NM_001143807.2:c.537_542=	NM_001143807.2:c.*542del	NM_001143807.2:c.*542dup	NM_001143807.2:c.541_542dup
BDNF transcript variant 9	NM_001143807.1:c.536_541=	NM_001143807.1:c.*541del	NM_001143807.1:c.*541dup	NM_001143807.1:c.540_541dup
BDNF transcript variant 8	NM_001143806.1:c.536_541=	NM_001143806.1:c.*541del	NM_001143806.1:c.*541dup	NM_001143806.1:c.540_541dup
BDNF transcript variant 7	NM_001143805.1:c.536_541=	NM_001143805.1:c.*541del	NM_001143805.1:c.*541dup	NM_001143805.1:c.540_541dup
BDNF transcript variant 15	NM_001143815.1:c.536_541=	NM_001143815.1:c.*541del	NM_001143815.1:c.*541dup	NM_001143815.1:c.540_541dup

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, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EGCUT_WGS	ss3675203690	Jul 13, 2019 (153)
2	GNOMAD	ss4232161628	Apr 26, 2021 (155)
3	GNOMAD	ss4232161629	Apr 26, 2021 (155)
4	TOPMED	ss4879424285	Apr 26, 2021 (155)
5	TOPMED	ss4879424286	Apr 26, 2021 (155)
6	TOPMED	ss4879424287	Apr 26, 2021 (155)
7	HUGCELL_USP	ss5482088960	Oct 16, 2022 (156)
8	1000G_HIGH_COVERAGE	ss5582177656	Oct 16, 2022 (156)
9	1000Genomes_30x	NC_000011.10 - 27657279	Oct 16, 2022 (156)
10	Genetic variation in the Estonian population	NC_000011.9 - 27678826	Oct 12, 2018 (152)
11	gnomAD - Genomes Submission ignored due to conflicting rows: Row 374846996 (NC_000011.10:27657278::C 4/139880) Row 374846997 (NC_000011.10:27657278:C: 3/139880)	-	Apr 26, 2021 (155)
12	gnomAD - Genomes Submission ignored due to conflicting rows: Row 374846996 (NC_000011.10:27657278::C 4/139880) Row 374846997 (NC_000011.10:27657278:C: 3/139880)	-	Apr 26, 2021 (155)
13	TopMed Submission ignored due to conflicting rows: Row 94969941 (NC_000011.10:27657278::C 5/264690) Row 94969942 (NC_000011.10:27657278::CC 1/264690) Row 94969943 (NC_000011.10:27657278:C: 6/264690)	-	Apr 26, 2021 (155)
14	TopMed Submission ignored due to conflicting rows: Row 94969941 (NC_000011.10:27657278::C 5/264690) Row 94969942 (NC_000011.10:27657278::CC 1/264690) Row 94969943 (NC_000011.10:27657278:C: 6/264690)	-	Apr 26, 2021 (155)
15	TopMed Submission ignored due to conflicting rows: Row 94969941 (NC_000011.10:27657278::C 5/264690) Row 94969942 (NC_000011.10:27657278::CC 1/264690) Row 94969943 (NC_000011.10:27657278:C: 6/264690)	-	Apr 26, 2021 (155)
16	ALFA	NC_000011.10 - 27657279	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
69703591, ss4232161629, ss4879424287, ss5482088960, ss5582177656	NC_000011.10:27657278:C:	NC_000011.10:27657278:CCCCCC:CCCCC	(self)
13871839873	NC_000011.10:27657278:CCCCCC:CCCCC	NC_000011.10:27657278:CCCCCC:CCCCC	(self)
20941938, ss3675203690	NC_000011.9:27678825::C	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCC	(self)
ss4232161628, ss4879424285	NC_000011.10:27657278::C	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCC	(self)
13871839873	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCC	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCC	(self)
ss4879424286	NC_000011.10:27657278::CC	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCCC	(self)
13871839873	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCCC	NC_000011.10:27657278:CCCCCC:CCCCC… NC_000011.10:27657278:CCCCCC:CCCCCCCC	(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 rs1262566140

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

rs1262566140