Name: rs1490929392
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.

rs1490929392

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:56518534-56518541 (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: del(TTA)₂ / delTTA
Variation Type: Indel Insertion and Deletion
Frequency: delTTA=0.000008 (2/264690, TOPMED)
delTTA=0.000014 (2/140240, GnomAD)
delTTA=0.00007 (1/14050, ALFA) (+ 1 more)
del(TTA)₂=0.0005 (1/1832, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BBS2 : 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	14050	TATTATTA=0.99993	TATTA=0.00007	0.999858	0.000142	0
European	Sub	9690	TATTATTA=0.9999	TATTA=0.0001	0.999794	0.000206	0
African	Sub	2898	TATTATTA=1.0000	TATTA=0.0000	1.0	0.0	N/A
African Others	Sub	114	TATTATTA=1.000	TATTA=0.000	1.0	0.0	N/A
African American	Sub	2784	TATTATTA=1.0000	TATTA=0.0000	1.0	0.0	N/A
Asian	Sub	112	TATTATTA=1.000	TATTA=0.000	1.0	0.0	N/A
East Asian	Sub	86	TATTATTA=1.00	TATTA=0.00	1.0	0.0	N/A
Other Asian	Sub	26	TATTATTA=1.00	TATTA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	TATTATTA=1.000	TATTA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TATTATTA=1.000	TATTA=0.000	1.0	0.0	N/A
South Asian	Sub	98	TATTATTA=1.00	TATTA=0.00	1.0	0.0	N/A
Other	Sub	496	TATTATTA=1.000	TATTA=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
TopMed	Global	Study-wide	264690	(TAT)₂TA=0.999992	delTTA=0.000008
gnomAD - Genomes	Global	Study-wide	140240	(TAT)₂TA=0.999986	delTTA=0.000014
gnomAD - Genomes	European	Sub	75948	(TAT)₂TA=0.99997	delTTA=0.00003
gnomAD - Genomes	African	Sub	42030	(TAT)₂TA=1.00000	delTTA=0.00000
gnomAD - Genomes	American	Sub	13652	(TAT)₂TA=1.00000	delTTA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	(TAT)₂TA=1.0000	delTTA=0.0000
gnomAD - Genomes	East Asian	Sub	3132	(TAT)₂TA=1.0000	delTTA=0.0000
gnomAD - Genomes	Other	Sub	2154	(TAT)₂TA=1.0000	delTTA=0.0000
Allele Frequency Aggregator	Total	Global	14050	(TAT)₂TA=0.99993	delTTA=0.00007
Allele Frequency Aggregator	European	Sub	9690	(TAT)₂TA=0.9999	delTTA=0.0001
Allele Frequency Aggregator	African	Sub	2898	(TAT)₂TA=1.0000	delTTA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(TAT)₂TA=1.000	delTTA=0.000
Allele Frequency Aggregator	Other	Sub	496	(TAT)₂TA=1.000	delTTA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(TAT)₂TA=1.000	delTTA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(TAT)₂TA=1.000	delTTA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(TAT)₂TA=1.00	delTTA=0.00
Korean Genome Project	KOREAN	Study-wide	1832	(TAT)₂TA=0.9995	del(TTA)₂=0.0005

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 16	NC_000016.10:g.56518536_56518541del
GRCh38.p14 chr 16	NC_000016.10:g.56518536TTA[1]
GRCh37.p13 chr 16	NC_000016.9:g.56552448_56552453del
GRCh37.p13 chr 16	NC_000016.9:g.56552448TTA[1]
BBS2 RefSeqGene	NG_009312.2:g.6486_6491del
BBS2 RefSeqGene	NG_009312.2:g.6486ATA[1]

Gene: BBS2, Bardet-Biedl syndrome 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BBS2 transcript variant 2	NM_001377456.1:c.117+1207… NM_001377456.1:c.117+1207_117+1212del	N/A	Intron Variant
BBS2 transcript variant 1	NM_031885.5:c.117+1207_11… NM_031885.5:c.117+1207_117+1212del	N/A	Intron Variant
BBS2 transcript variant 3	NR_165293.1:n.	N/A	Intron Variant
BBS2 transcript variant 4	NR_165294.1:n.	N/A	Intron Variant
BBS2 transcript variant 5	NR_165295.1:n.	N/A	Intron Variant
BBS2 transcript variant 6	NR_165296.1:n.	N/A	Intron Variant
BBS2 transcript variant 7	NR_165297.1:n.	N/A	Intron Variant
BBS2 transcript variant X1	XM_047434412.1:c.117+1207… XM_047434412.1:c.117+1207_117+1212del	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	(TAT)₂TA=	del(TTA)₂	delTTA
GRCh38.p14 chr 16	NC_000016.10:g.56518534_56518541=	NC_000016.10:g.56518536_56518541del	NC_000016.10:g.56518536TTA[1]
GRCh37.p13 chr 16	NC_000016.9:g.56552446_56552453=	NC_000016.9:g.56552448_56552453del	NC_000016.9:g.56552448TTA[1]
BBS2 RefSeqGene	NG_009312.2:g.6484_6491=	NG_009312.2:g.6486_6491del	NG_009312.2:g.6486ATA[1]
BBS2 transcript variant 2	NM_001377456.1:c.117+1212=	NM_001377456.1:c.117+1207_117+1212del	NM_001377456.1:c.117+1210_117+1212del
BBS2 transcript	NM_031885.3:c.117+1212=	NM_031885.3:c.117+1207_117+1212del	NM_031885.3:c.117+1210_117+1212del
BBS2 transcript variant 1	NM_031885.5:c.117+1212=	NM_031885.5:c.117+1207_117+1212del	NM_031885.5:c.117+1210_117+1212del
BBS2 transcript variant X1	XM_005256080.1:c.117+1212=	XM_005256080.1:c.117+1207_117+1212del	XM_005256080.1:c.117+1210_117+1212del
BBS2 transcript variant X2	XM_005256081.1:c.117+1212=	XM_005256081.1:c.117+1207_117+1212del	XM_005256081.1:c.117+1210_117+1212del
BBS2 transcript variant X3	XM_005256082.1:c.117+1212=	XM_005256082.1:c.117+1207_117+1212del	XM_005256082.1:c.117+1210_117+1212del
BBS2 transcript variant X1	XM_047434412.1:c.117+1212=	XM_047434412.1:c.117+1207_117+1212del	XM_047434412.1:c.117+1210_117+1212del

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, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2943377321	Nov 08, 2017 (151)
2	KOGIC	ss3977650413	Apr 27, 2020 (154)
3	TOPMED	ss5016510256	Apr 26, 2021 (155)
4	gnomAD - Genomes	NC_000016.10 - 56518534	Apr 26, 2021 (155)
5	Korean Genome Project	NC_000016.10 - 56518534	Apr 27, 2020 (154)
6	TopMed	NC_000016.10 - 56518534	Apr 26, 2021 (155)
7	ALFA	NC_000016.10 - 56518534	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
34028414, ss3977650413	NC_000016.10:56518533:TATTAT:	NC_000016.10:56518533:TATTATTA:TA	(self)
ss2943377321	NC_000016.9:56552445:TAT:	NC_000016.10:56518533:TATTATTA:TAT… NC_000016.10:56518533:TATTATTA:TATTA	(self)
490504486, 232055917, ss5016510256	NC_000016.10:56518533:TAT:	NC_000016.10:56518533:TATTATTA:TAT… NC_000016.10:56518533:TATTATTA:TATTA	(self)
2704827829	NC_000016.10:56518533:TATTATTA:TAT… NC_000016.10:56518533:TATTATTA:TATTA	NC_000016.10:56518533:TATTATTA:TAT… NC_000016.10:56518533:TATTATTA:TATTA	(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 rs1490929392

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

rs1490929392