Name: rs1491370090
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.

rs1491370090

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:84149709-84149711 (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: delCA
Variation Type: Indel Insertion and Deletion
Frequency: delCA=0.000281 (39/138930, GnomAD)
delCA=0.00014 (4/28258, 14KJPN)
delCA=0.00024 (4/16760, 8.3KJPN) (+ 1 more)
delCA=0.00025 (3/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DNAAF1 : 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	ACA=0.99975	A=0.00025	0.999494	0.000506	0
European	Sub	7618	ACA=0.9999	A=0.0001	0.999737	0.000263	0
African	Sub	2816	ACA=0.9996	A=0.0004	0.99929	0.00071	0
African Others	Sub	108	ACA=1.000	A=0.000	1.0	0.0	N/A
African American	Sub	2708	ACA=0.9996	A=0.0004	0.999261	0.000739	0
Asian	Sub	108	ACA=1.000	A=0.000	1.0	0.0	N/A
East Asian	Sub	84	ACA=1.00	A=0.00	1.0	0.0	N/A
Other Asian	Sub	24	ACA=1.00	A=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	ACA=1.000	A=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	ACA=0.998	A=0.002	0.996721	0.003279	0
South Asian	Sub	94	ACA=1.00	A=0.00	1.0	0.0	N/A
Other	Sub	470	ACA=1.000	A=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	138930	ACA=0.999719	delCA=0.000281
gnomAD - Genomes	European	Sub	75468	ACA=0.99977	delCA=0.00023
gnomAD - Genomes	African	Sub	41418	ACA=0.99949	delCA=0.00051
gnomAD - Genomes	American	Sub	13494	ACA=0.99993	delCA=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3310	ACA=1.0000	delCA=0.0000
gnomAD - Genomes	East Asian	Sub	3114	ACA=1.0000	delCA=0.0000
gnomAD - Genomes	Other	Sub	2126	ACA=1.0000	delCA=0.0000
14KJPN	JAPANESE	Study-wide	28258	ACA=0.99986	delCA=0.00014
8.3KJPN	JAPANESE	Study-wide	16760	ACA=0.99976	delCA=0.00024
Allele Frequency Aggregator	Total	Global	11862	ACA=0.99975	delCA=0.00025
Allele Frequency Aggregator	European	Sub	7618	ACA=0.9999	delCA=0.0001
Allele Frequency Aggregator	African	Sub	2816	ACA=0.9996	delCA=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	610	ACA=0.998	delCA=0.002
Allele Frequency Aggregator	Other	Sub	470	ACA=1.000	delCA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	ACA=1.000	delCA=0.000
Allele Frequency Aggregator	Asian	Sub	108	ACA=1.000	delCA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	ACA=1.00	delCA=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.84149710_84149711del
GRCh37.p13 chr 16	NC_000016.9:g.84183315_84183316del
DNAAF1 RefSeqGene	NG_021174.2:g.9404_9405del
DNAAF1 RefSeqGene	NG_021174.1:g.9451_9452del

Gene: DNAAF1, dynein axonemal assembly factor 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DNAAF1 transcript variant 1	NM_178452.6:c.261-541_261… NM_178452.6:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant 2	NM_001318756.1:c.	N/A	Genic Upstream Transcript Variant
DNAAF1 transcript variant X5	XM_006721129.4:c.261-541_… XM_006721129.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X1	XM_011522853.4:c.261-541_… XM_011522853.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X3	XM_011522854.4:c.261-541_… XM_011522854.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X4	XM_011522855.4:c.261-541_… XM_011522855.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X8	XM_011522857.4:c.261-541_… XM_011522857.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X9	XM_011522858.4:c.261-541_… XM_011522858.4:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X2	XM_017022918.3:c.261-541_… XM_017022918.3:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X10	XM_017022919.2:c.-1-541_-… XM_017022919.2:c.-1-541_-1-540del	N/A	Intron Variant
DNAAF1 transcript variant X6	XM_047433589.1:c.261-541_… XM_047433589.1:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X7	XM_047433590.1:c.261-541_… XM_047433590.1:c.261-541_261-540del	N/A	Intron Variant
DNAAF1 transcript variant X11	XM_017022920.3:c.	N/A	Genic Upstream Transcript 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	ACA=	delCA
GRCh38.p14 chr 16	NC_000016.10:g.84149709_84149711=	NC_000016.10:g.84149710_84149711del
GRCh37.p13 chr 16	NC_000016.9:g.84183314_84183316=	NC_000016.9:g.84183315_84183316del
DNAAF1 RefSeqGene	NG_021174.2:g.9403_9405=	NG_021174.2:g.9404_9405del
DNAAF1 RefSeqGene	NG_021174.1:g.9450_9452=	NG_021174.1:g.9451_9452del
DNAAF1 transcript	NM_178452.4:c.261-542=	NM_178452.4:c.261-541_261-540del
DNAAF1 transcript variant 1	NM_178452.6:c.261-542=	NM_178452.6:c.261-541_261-540del
DNAAF1 transcript variant X1	XM_005255793.1:c.261-542=	XM_005255793.1:c.261-541_261-540del
DNAAF1 transcript variant X5	XM_006721129.4:c.261-542=	XM_006721129.4:c.261-541_261-540del
DNAAF1 transcript variant X1	XM_011522853.4:c.261-542=	XM_011522853.4:c.261-541_261-540del
DNAAF1 transcript variant X3	XM_011522854.4:c.261-542=	XM_011522854.4:c.261-541_261-540del
DNAAF1 transcript variant X4	XM_011522855.4:c.261-542=	XM_011522855.4:c.261-541_261-540del
DNAAF1 transcript variant X8	XM_011522857.4:c.261-542=	XM_011522857.4:c.261-541_261-540del
DNAAF1 transcript variant X9	XM_011522858.4:c.261-542=	XM_011522858.4:c.261-541_261-540del
DNAAF1 transcript variant X2	XM_017022918.3:c.261-542=	XM_017022918.3:c.261-541_261-540del
DNAAF1 transcript variant X10	XM_017022919.2:c.-1-542=	XM_017022919.2:c.-1-541_-1-540del
DNAAF1 transcript variant X6	XM_047433589.1:c.261-542=	XM_047433589.1:c.261-541_261-540del
DNAAF1 transcript variant X7	XM_047433590.1:c.261-542=	XM_047433590.1:c.261-541_261-540del

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	ss2946007362	Jan 10, 2018 (151)
2	TOMMO_GENOMICS	ss5220776052	Apr 27, 2021 (155)
3	TOMMO_GENOMICS	ss5776133720	Oct 17, 2022 (156)
4	gnomAD - Genomes	NC_000016.10 - 84149709	Apr 27, 2021 (155)
5	8.3KJPN	NC_000016.9 - 84183314	Apr 27, 2021 (155)
6	14KJPN	NC_000016.10 - 84149709	Oct 17, 2022 (156)
7	ALFA	NC_000016.10 - 84149709	Apr 27, 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
78745359, ss2946007362, ss5220776052	NC_000016.9:84183313:AC:	NC_000016.10:84149708:ACA:A	(self)
497252405, 109970824, ss5776133720	NC_000016.10:84149708:AC:	NC_000016.10:84149708:ACA:A	(self)
12383107424	NC_000016.10:84149708:ACA:A	NC_000016.10:84149708:ACA: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 rs1491370090

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491370090