Name: rs1491279870
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.

rs1491279870

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:30630940-30630941 (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: insC / insCTC
Variation Type: Insertion
Frequency: insC=0.00009 (9/98448, GnomAD)
insC=0.00014 (4/28258, 14KJPN)
insC=0.00024 (4/16754, 8.3KJPN) (+ 2 more)
insC=0.00000 (0/11862, ALFA)
insCTC=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LYZL2 : 2KB Upstream 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	HWEP
Total	Global	11862	=1.00000	C=0.00000, CTC=0.00000	1.0	N/A
European	Sub	7618	=1.0000	C=0.0000, CTC=0.0000	1.0	N/A
African	Sub	2816	=1.0000	C=0.0000, CTC=0.0000	1.0	N/A
African Others	Sub	108	=1.000	C=0.000, CTC=0.000	1.0	N/A
African American	Sub	2708	=1.0000	C=0.0000, CTC=0.0000	1.0	N/A
Asian	Sub	108	=1.000	C=0.000, CTC=0.000	1.0	N/A
East Asian	Sub	84	=1.00	C=0.00, CTC=0.00	1.0	N/A
Other Asian	Sub	24	=1.00	C=0.00, CTC=0.00	1.0	N/A
Latin American 1	Sub	146	=1.000	C=0.000, CTC=0.000	1.0	N/A
Latin American 2	Sub	610	=1.000	C=0.000, CTC=0.000	1.0	N/A
South Asian	Sub	94	=1.00	C=0.00, CTC=0.00	1.0	N/A
Other	Sub	470	=1.000	C=0.000, CTC=0.000	1.0	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	98448	- No frequency provided	insC=0.00009
gnomAD - Genomes	European	Sub	47286	- No frequency provided	insC=0.00006
gnomAD - Genomes	African	Sub	34538	- No frequency provided	insC=0.00000
gnomAD - Genomes	American	Sub	9896	- No frequency provided	insC=0.0000
gnomAD - Genomes	East Asian	Sub	3012	- No frequency provided	insC=0.0017
gnomAD - Genomes	Ashkenazi Jewish	Sub	2216	- No frequency provided	insC=0.0005
gnomAD - Genomes	Other	Sub	1500	- No frequency provided	insC=0.0000
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	insC=0.00014
8.3KJPN	JAPANESE	Study-wide	16754	- No frequency provided	insC=0.00024
Allele Frequency Aggregator	Total	Global	11862	- No frequency provided	insC=0.00000, insCTC=0.00000
Allele Frequency Aggregator	European	Sub	7618	- No frequency provided	insC=0.0000, insCTC=0.0000
Allele Frequency Aggregator	African	Sub	2816	- No frequency provided	insC=0.0000, insCTC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	- No frequency provided	insC=0.000, insCTC=0.000
Allele Frequency Aggregator	Other	Sub	470	- No frequency provided	insC=0.000, insCTC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	- No frequency provided	insC=0.000, insCTC=0.000
Allele Frequency Aggregator	Asian	Sub	108	- No frequency provided	insC=0.000, insCTC=0.000
Allele Frequency Aggregator	South Asian	Sub	94	- No frequency provided	insC=0.00, insCTC=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 10	NC_000010.11:g.30630940_30630941insC
GRCh38.p14 chr 10	NC_000010.11:g.30630940_30630941insCTC
GRCh37.p13 chr 10	NC_000010.10:g.30919869_30919870insC
GRCh37.p13 chr 10	NC_000010.10:g.30919869_30919870insCTC

Gene: LYZL2, lysozyme like 2 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LYZL2 transcript	NM_183058.3:c.	N/A	Upstream Transcript Variant
LYZL2 transcript variant X1	XM_011519306.3:c.	N/A	Upstream Transcript Variant
LYZL2 transcript variant X2	XM_011519307.3:c.	N/A	Upstream Transcript Variant
LYZL2 transcript variant X3	XR_930469.3:n.	N/A	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	=	insC	insCTC
GRCh38.p14 chr 10	NC_000010.11:g.30630940_30630941=	NC_000010.11:g.30630940_30630941insC	NC_000010.11:g.30630940_30630941insCTC
GRCh37.p13 chr 10	NC_000010.10:g.30919869_30919870=	NC_000010.10:g.30919869_30919870insC	NC_000010.10:g.30919869_30919870insCTC

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, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2887212196	Jan 10, 2018 (151)
2	TOMMO_GENOMICS	ss5196959960	Apr 26, 2021 (155)
3	TOMMO_GENOMICS	ss5742013783	Oct 16, 2022 (156)
4	YY_MCH	ss5811339825	Oct 16, 2022 (156)
5	gnomAD - Genomes	NC_000010.11 - 30630941	Apr 26, 2021 (155)
6	8.3KJPN	NC_000010.10 - 30919870	Apr 26, 2021 (155)
7	14KJPN	NC_000010.11 - 30630941	Oct 16, 2022 (156)
8	ALFA	NC_000010.11 - 30630941	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
54929267, ss2887212196, ss5196959960	NC_000010.10:30919869::C	NC_000010.11:30630940::C	(self)
347779139, 75850887, 3348626585, ss5742013783, ss5811339825	NC_000010.11:30630940::C	NC_000010.11:30630940::C	(self)
3348626585	NC_000010.11:30630940::CTC	NC_000010.11:30630940::CTC	(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 rs1491279870

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

rs1491279870