Name: rs1491422993
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.

rs1491422993

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:47403413-47403420 (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: dupA
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.000122 (17/139368, GnomAD)
dupA=0.00074 (21/28258, 14KJPN)
dupA=0.00016 (3/18520, ALFA) (+ 2 more)
dupA=0.00089 (15/16760, 8.3KJPN)
dupA=0.0004 (2/4480, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ITFG1 : 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	18520	AAAAAAAA=0.99984	AAAAAAAAA=0.00016	0.999676	0.000324	0
European	Sub	14152	AAAAAAAA=0.99986	AAAAAAAAA=0.00014	0.999717	0.000283	0
African	Sub	2898	AAAAAAAA=1.0000	AAAAAAAAA=0.0000	1.0	0.0	N/A
African Others	Sub	114	AAAAAAAA=1.000	AAAAAAAAA=0.000	1.0	0.0	N/A
African American	Sub	2784	AAAAAAAA=1.0000	AAAAAAAAA=0.0000	1.0	0.0	N/A
Asian	Sub	112	AAAAAAAA=0.991	AAAAAAAAA=0.009	0.982143	0.017857	0
East Asian	Sub	86	AAAAAAAA=0.99	AAAAAAAAA=0.01	0.976744	0.023256	0
Other Asian	Sub	26	AAAAAAAA=1.00	AAAAAAAAA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	AAAAAAAA=1.000	AAAAAAAAA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	AAAAAAAA=1.000	AAAAAAAAA=0.000	1.0	0.0	N/A
South Asian	Sub	98	AAAAAAAA=1.00	AAAAAAAAA=0.00	1.0	0.0	N/A
Other	Sub	504	AAAAAAAA=1.000	AAAAAAAAA=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	139368	- No frequency provided	dupA=0.000122
gnomAD - Genomes	European	Sub	75406	- No frequency provided	dupA=0.00007
gnomAD - Genomes	African	Sub	41818	- No frequency provided	dupA=0.00007
gnomAD - Genomes	American	Sub	13566	- No frequency provided	dupA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	- No frequency provided	dupA=0.0000
gnomAD - Genomes	East Asian	Sub	3124	- No frequency provided	dupA=0.0029
gnomAD - Genomes	Other	Sub	2136	- No frequency provided	dupA=0.0000
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupA=0.00074
Allele Frequency Aggregator	Total	Global	18520	(A)₈=0.99984	dupA=0.00016
Allele Frequency Aggregator	European	Sub	14152	(A)₈=0.99986	dupA=0.00014
Allele Frequency Aggregator	African	Sub	2898	(A)₈=1.0000	dupA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₈=1.000	dupA=0.000
Allele Frequency Aggregator	Other	Sub	504	(A)₈=1.000	dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₈=1.000	dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₈=0.991	dupA=0.009
Allele Frequency Aggregator	South Asian	Sub	98	(A)₈=1.00	dupA=0.00
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupA=0.00089
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupA=0.0004

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.47403420dup
GRCh37.p13 chr 16	NC_000016.9:g.47437331dup

Gene: ITFG1, integrin alpha FG-GAP repeat containing 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ITFG1 transcript variant 2	NM_001305002.2:c.316+2539… NM_001305002.2:c.316+25391dup	N/A	Intron Variant
ITFG1 transcript variant 1	NM_030790.5:c.655+25391dup	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	(A)₈=	dupA
GRCh38.p14 chr 16	NC_000016.10:g.47403413_47403420=	NC_000016.10:g.47403420dup
GRCh37.p13 chr 16	NC_000016.9:g.47437324_47437331=	NC_000016.9:g.47437331dup
ITFG1 transcript variant 2	NM_001305002.2:c.316+25391=	NM_001305002.2:c.316+25391dup
ITFG1 transcript	NM_030790.3:c.655+25391=	NM_030790.3:c.655+25391dup
ITFG1 transcript variant 1	NM_030790.5:c.655+25391=	NM_030790.5:c.655+25391dup

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	ss3014464488	Jan 10, 2018 (151)
2	EGCUT_WGS	ss3681436685	Jul 13, 2019 (153)
3	GNOMAD	ss4300429784	Apr 26, 2021 (155)
4	TOMMO_GENOMICS	ss5219427059	Apr 26, 2021 (155)
5	1000G_HIGH_COVERAGE	ss5300847407	Oct 17, 2022 (156)
6	TOMMO_GENOMICS	ss5774395406	Oct 17, 2022 (156)
7	YY_MCH	ss5815947218	Oct 17, 2022 (156)
8	EVA	ss5898962940	Oct 17, 2022 (156)
9	Genetic variation in the Estonian population	NC_000016.9 - 47437324	Oct 12, 2018 (152)
10	gnomAD - Genomes	NC_000016.10 - 47403413	Apr 26, 2021 (155)
11	8.3KJPN	NC_000016.9 - 47437324	Apr 26, 2021 (155)
12	14KJPN	NC_000016.10 - 47403413	Oct 17, 2022 (156)
13	ALFA	NC_000016.10 - 47403413	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
27174933, 77396366, ss3014464488, ss3681436685, ss5219427059	NC_000016.9:47437323::A	NC_000016.10:47403412:AAAAAAAA:AAA… NC_000016.10:47403412:AAAAAAAA:AAAAAAAAA	(self)
488615978, 108232510, ss4300429784, ss5300847407, ss5774395406, ss5815947218, ss5898962940	NC_000016.10:47403412::A	NC_000016.10:47403412:AAAAAAAA:AAA… NC_000016.10:47403412:AAAAAAAA:AAAAAAAAA	(self)
13494036946	NC_000016.10:47403412:AAAAAAAA:AAA… NC_000016.10:47403412:AAAAAAAA:AAAAAAAAA	NC_000016.10:47403412:AAAAAAAA:AAA… NC_000016.10:47403412:AAAAAAAA:AAAAAAAAA	(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 rs1491422993

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

rs1491422993