Name: rs1490211245
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.

rs1490211245

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:29450896-29450901 (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: delTAT
Variation Type: Indel Insertion and Deletion
Frequency: delTAT=0.01159 (621/53564, GnomAD)
delTAT=0.00590 (70/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BOLA2-SMG1P6 : 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	TATTAT=0.99410	TAT=0.00590	0.988198	0.011802	0
European	Sub	7618	TATTAT=0.9997	TAT=0.0003	0.999475	0.000525	0
African	Sub	2816	TATTAT=0.9766	TAT=0.0234	0.953125	0.046875	1
African Others	Sub	108	TATTAT=0.954	TAT=0.046	0.907407	0.092593	0
African American	Sub	2708	TATTAT=0.9775	TAT=0.0225	0.954948	0.045052	0
Asian	Sub	108	TATTAT=1.000	TAT=0.000	1.0	0.0	N/A
East Asian	Sub	84	TATTAT=1.00	TAT=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TATTAT=1.00	TAT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	TATTAT=1.000	TAT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TATTAT=0.997	TAT=0.003	0.993443	0.006557	0
South Asian	Sub	94	TATTAT=1.00	TAT=0.00	1.0	0.0	N/A
Other	Sub	470	TATTAT=1.000	TAT=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	53564	(TAT)₂=0.98841	delTAT=0.01159
gnomAD - Genomes	European	Sub	31318	(TAT)₂=0.99974	delTAT=0.00026
gnomAD - Genomes	African	Sub	15770	(TAT)₂=0.96303	delTAT=0.03697
gnomAD - Genomes	American	Sub	2716	(TAT)₂=0.9919	delTAT=0.0081
gnomAD - Genomes	Ashkenazi Jewish	Sub	1926	(TAT)₂=0.9990	delTAT=0.0010
gnomAD - Genomes	East Asian	Sub	1238	(TAT)₂=1.0000	delTAT=0.0000
gnomAD - Genomes	Other	Sub	596	(TAT)₂=0.990	delTAT=0.010
Allele Frequency Aggregator	Total	Global	11862	(TAT)₂=0.99410	delTAT=0.00590
Allele Frequency Aggregator	European	Sub	7618	(TAT)₂=0.9997	delTAT=0.0003
Allele Frequency Aggregator	African	Sub	2816	(TAT)₂=0.9766	delTAT=0.0234
Allele Frequency Aggregator	Latin American 2	Sub	610	(TAT)₂=0.997	delTAT=0.003
Allele Frequency Aggregator	Other	Sub	470	(TAT)₂=1.000	delTAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(TAT)₂=1.000	delTAT=0.000
Allele Frequency Aggregator	Asian	Sub	108	(TAT)₂=1.000	delTAT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(TAT)₂=1.00	delTAT=0.00

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.29450896TAT[1]
GRCh37.p13 chr 16	NC_000016.9:g.29462217TAT[1]

Gene: BOLA2-SMG1P6, BOLA2-SMG1P6 readthrough (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BOLA2-SMG1P6 transcript variant 1	NM_001320622.1:c.321+3118… NM_001320622.1:c.321+3118_321+3120del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 2	NM_001320623.1:c.359+3118… NM_001320623.1:c.359+3118_359+3120del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 3	NM_001320624.1:c.261+3293… NM_001320624.1:c.261+3293_261+3295del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 4	NM_001320625.1:c.5+3293_5… NM_001320625.1:c.5+3293_5+3295del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 5	NM_001320627.1:c.-16+3118… NM_001320627.1:c.-16+3118_-16+3120del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 6	NM_001320628.1:c.-16+3118… NM_001320628.1:c.-16+3118_-16+3120del	N/A	Intron Variant
BOLA2-SMG1P6 transcript variant 7	NR_135316.1: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	(TAT)₂=	delTAT
GRCh38.p14 chr 16	NC_000016.10:g.29450896_29450901=	NC_000016.10:g.29450896TAT[1]
GRCh37.p13 chr 16	NC_000016.9:g.29462217_29462222=	NC_000016.9:g.29462217TAT[1]
BOLA2-SMG1P6 transcript variant 1	NM_001320622.1:c.321+3120=	NM_001320622.1:c.321+3118_321+3120del
BOLA2-SMG1P6 transcript variant 2	NM_001320623.1:c.359+3120=	NM_001320623.1:c.359+3118_359+3120del
BOLA2-SMG1P6 transcript variant 3	NM_001320624.1:c.261+3295=	NM_001320624.1:c.261+3293_261+3295del
BOLA2-SMG1P6 transcript variant 4	NM_001320625.1:c.5+3295=	NM_001320625.1:c.5+3293_5+3295del
BOLA2-SMG1P6 transcript variant 5	NM_001320627.1:c.-16+3120=	NM_001320627.1:c.-16+3118_-16+3120del
BOLA2-SMG1P6 transcript variant 6	NM_001320628.1:c.-16+3120=	NM_001320628.1:c.-16+3118_-16+3120del
BOLA2 transcript variant X1	XM_005255415.1:c.359+3120=	XM_005255415.1:c.359+3118_359+3120del
BOLA2 transcript variant X2	XM_005255416.1:c.-16+3120=	XM_005255416.1:c.-16+3118_-16+3120del

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#.

2 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4299340531	Apr 26, 2021 (155)
2	1000G_HIGH_COVERAGE	ss5300654982	Oct 16, 2022 (156)
3	gnomAD - Genomes	NC_000016.10 - 29450896	Apr 26, 2021 (155)
4	ALFA	NC_000016.10 - 29450896	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
487002438, ss4299340531, ss5300654982	NC_000016.10:29450895:TAT:	NC_000016.10:29450895:TATTAT:TAT	(self)
2630190289	NC_000016.10:29450895:TATTAT:TAT	NC_000016.10:29450895:TATTAT:TAT	(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 rs1490211245

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

rs1490211245