Name: rs1490823893
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.

rs1490823893

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:77761107-77761108 (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=0.000007 (1/140316, GnomAD)
dupA=0.00008 (1/12518, GO-ESP)
dupA=0.0000 (0/6396, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C14orf178 : Non Coding Transcript Variant
SNW1 : 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	Alt HMOZ	HTRZ	HWEP
Total	Global	6396	AA=1.0000	AAA=0.0000	1.0	0.0	0.0	N/A
European	Sub	6146	AA=1.0000	AAA=0.0000	1.0	0.0	0.0	N/A
African	Sub	0	AA=0	AAA=0	0	0	0	N/A
African Others	Sub	0	AA=0	AAA=0	0	0	0	N/A
African American	Sub	0	AA=0	AAA=0	0	0	0	N/A
Asian	Sub	0	AA=0	AAA=0	0	0	0	N/A
East Asian	Sub	0	AA=0	AAA=0	0	0	0	N/A
Other Asian	Sub	0	AA=0	AAA=0	0	0	0	N/A
Latin American 1	Sub	0	AA=0	AAA=0	0	0	0	N/A
Latin American 2	Sub	0	AA=0	AAA=0	0	0	0	N/A
South Asian	Sub	0	AA=0	AAA=0	0	0	0	N/A
Other	Sub	250	AA=1.000	AAA=0.000	1.0	0.0	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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	140316	- No frequency provided	dupA=0.000007
gnomAD - Genomes	European	Sub	75968	- No frequency provided	dupA=0.00001
gnomAD - Genomes	African	Sub	42070	- No frequency provided	dupA=0.00000
gnomAD - Genomes	American	Sub	13668	- No frequency provided	dupA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	- No frequency provided	dupA=0.0000
gnomAD - Genomes	East Asian	Sub	3134	- No frequency provided	dupA=0.0000
gnomAD - Genomes	Other	Sub	2154	- No frequency provided	dupA=0.0000
GO Exome Sequencing Project	Global	Study-wide	12518	- No frequency provided	dupA=0.00008
GO Exome Sequencing Project	European American	Sub	8254	- No frequency provided	dupA=0.0001
GO Exome Sequencing Project	African American	Sub	4264	- No frequency provided	dupA=0.0000
Allele Frequency Aggregator	Total	Global	6396	AA=1.0000	dupA=0.0000
Allele Frequency Aggregator	European	Sub	6146	AA=1.0000	dupA=0.0000
Allele Frequency Aggregator	Other	Sub	250	AA=1.000	dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	0	AA=0	dupA=0
Allele Frequency Aggregator	Latin American 2	Sub	0	AA=0	dupA=0
Allele Frequency Aggregator	South Asian	Sub	0	AA=0	dupA=0
Allele Frequency Aggregator	African	Sub	0	AA=0	dupA=0
Allele Frequency Aggregator	Asian	Sub	0	AA=0	dupA=0

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 14	NC_000014.9:g.77761108dup
GRCh37.p13 chr 14	NC_000014.8:g.78227451dup

Gene: SNW1, SNW domain containing 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNW1 transcript variant 1	NM_001318844.2:c.14+7dup	N/A	Intron Variant
SNW1 transcript variant 2	NM_012245.3:c.14+7dup	N/A	Intron Variant
SNW1 transcript variant X1	XM_047431112.1:c.14+7dup	N/A	Intron Variant

Gene: C14orf178, chromosome 14 open reading frame 178 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLIRP-OT1 transcript variant 2	NR_161324.1:n.341dup	N/A	Non Coding Transcript Variant
SLIRP-OT1 transcript variant 1	NR_161323.1:n.341dup	N/A	Non Coding 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	AA=	dupA
GRCh38.p14 chr 14	NC_000014.9:g.77761107_77761108=	NC_000014.9:g.77761108dup
GRCh37.p13 chr 14	NC_000014.8:g.78227450_78227451=	NC_000014.8:g.78227451dup
C14orf178 transcript variant 1	NM_174943.3:c.65_66=	NM_174943.3:c.66dup
SLIRP-OT1 transcript variant 1	NR_161323.1:n.340_341=	NR_161323.1:n.341dup
SLIRP-OT1 transcript variant 2	NR_161324.1:n.340_341=	NR_161324.1:n.341dup
C14orf178 transcript variant 2	NM_001173978.1:c.-12_-11=	NM_001173978.1:c.-11dup
SNW1 transcript variant 1	NM_001318844.2:c.14+7=	NM_001318844.2:c.14+7dup
SNW1 transcript variant 2	NM_012245.2:c.14+7=	NM_012245.2:c.14+7dup
SNW1 transcript variant 2	NM_012245.3:c.14+7=	NM_012245.3:c.14+7dup
uncharacterized protein C14orf178 isoform 1	NP_777603.1:p.Gln22=	NP_777603.1:p.Pro23fs
SNW1 transcript variant X1	XM_005267413.1:c.14+7=	XM_005267413.1:c.14+7dup
SNW1 transcript variant X2	XM_005267414.1:c.14+7=	XM_005267414.1:c.14+7dup
SNW1 transcript variant X1	XM_047431112.1:c.14+7=	XM_047431112.1:c.14+7dup

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#.

4 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	AFFY	ss2985027347	Nov 08, 2017 (151)
2	ILLUMINA	ss3653798589	Oct 12, 2018 (152)
3	EVA	ss3824870247	Apr 27, 2020 (154)
4	GNOMAD	ss4281191131	Apr 27, 2021 (155)
5	gnomAD - Genomes	NC_000014.9 - 77761107	Apr 27, 2021 (155)
6	GO Exome Sequencing Project	NC_000014.8 - 78227450	Oct 12, 2018 (152)
7	ALFA	NC_000014.9 - 77761107	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
1327561, ss2985027347, ss3653798589, ss3824870247	NC_000014.8:78227449::A	NC_000014.9:77761106:AA:AAA	(self)
456440548, ss4281191131	NC_000014.9:77761106::A	NC_000014.9:77761106:AA:AAA	(self)
4818573308	NC_000014.9:77761106:AA:AAA	NC_000014.9:77761106:AA:AAA	(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 rs1490823893

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

rs1490823893