Name: rs1491465420
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.

rs1491465420

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:27178518-27178520 (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=0.00039 (11/28012, 14KJPN)
delCA=0.00858 (104/12120, GnomAD)
delCA=0.01155 (137/11862, ALFA) (+ 1 more)
delCA=0.0051 (8/1570, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105379340 : 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=0.98845	A=0.01155	0.976901	0.023099	0
European	Sub	7618	ACA=0.9875	A=0.0125	0.975059	0.024941	0
African	Sub	2816	ACA=0.9901	A=0.0099	0.980114	0.019886	0
African Others	Sub	108	ACA=0.991	A=0.009	0.981481	0.018519	0
African American	Sub	2708	ACA=0.9900	A=0.0100	0.980059	0.019941	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=0.986	A=0.014	0.972603	0.027397	0
Latin American 2	Sub	610	ACA=0.995	A=0.005	0.990164	0.009836	0
South Asian	Sub	94	ACA=0.98	A=0.02	0.957447	0.042553	0
Other	Sub	470	ACA=0.985	A=0.015	0.970213	0.029787	0

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
14KJPN	JAPANESE	Study-wide	28012	ACA=0.99961	delCA=0.00039
gnomAD - Genomes	Global	Study-wide	12120	ACA=0.99142	delCA=0.00858
gnomAD - Genomes	African	Sub	10390	ACA=0.99220	delCA=0.00780
gnomAD - Genomes	European	Sub	994	ACA=0.982	delCA=0.018
gnomAD - Genomes	American	Sub	474	ACA=0.994	delCA=0.006
gnomAD - Genomes	Other	Sub	144	ACA=0.993	delCA=0.007
gnomAD - Genomes	East Asian	Sub	76	ACA=1.00	delCA=0.00
gnomAD - Genomes	Ashkenazi Jewish	Sub	42	ACA=0.98	delCA=0.02
Allele Frequency Aggregator	Total	Global	11862	ACA=0.98845	delCA=0.01155
Allele Frequency Aggregator	European	Sub	7618	ACA=0.9875	delCA=0.0125
Allele Frequency Aggregator	African	Sub	2816	ACA=0.9901	delCA=0.0099
Allele Frequency Aggregator	Latin American 2	Sub	610	ACA=0.995	delCA=0.005
Allele Frequency Aggregator	Other	Sub	470	ACA=0.985	delCA=0.015
Allele Frequency Aggregator	Latin American 1	Sub	146	ACA=0.986	delCA=0.014
Allele Frequency Aggregator	Asian	Sub	108	ACA=1.000	delCA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	ACA=0.98	delCA=0.02
Korean Genome Project	KOREAN	Study-wide	1570	ACA=0.9949	delCA=0.0051

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 8	NC_000008.11:g.27178519_27178520del
GRCh37.p13 chr 8	NC_000008.10:g.27036036_27036037del

Gene: LOC105379340, uncharacterized LOC105379340 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105379340 transcript	XR_949607.3: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	ACA=	delCA
GRCh38.p14 chr 8	NC_000008.11:g.27178518_27178520=	NC_000008.11:g.27178519_27178520del
GRCh37.p13 chr 8	NC_000008.10:g.27036035_27036037=	NC_000008.10:g.27036036_27036037del

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#.

9 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss500142343	Jan 10, 2018 (151)
2	HAMMER_LAB	ss1805460647	Jan 10, 2018 (151)
3	GNOMAD	ss2864730956	Jan 10, 2018 (151)
4	EVA_DECODE	ss3721673318	Jul 13, 2019 (153)
5	KOGIC	ss3963519129	Apr 26, 2020 (154)
6	SANFORD_IMAGENETICS	ss5645038942	Oct 16, 2022 (156)
7	TOMMO_GENOMICS	ss5729599329	Oct 16, 2022 (156)
8	EVA	ss5888255372	Oct 16, 2022 (156)
9	EVA	ss5974225276	Oct 16, 2022 (156)
10	gnomAD - Genomes	NC_000008.11 - 27178518	Apr 26, 2021 (155)
11	Korean Genome Project	NC_000008.11 - 27178518	Apr 26, 2020 (154)
12	14KJPN	NC_000008.11 - 27178518	Oct 16, 2022 (156)
13	ALFA	NC_000008.11 - 27178518	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
ss500142343, ss1805460647, ss2864730956, ss5645038942, ss5974225276	NC_000008.10:27036034:AC:	NC_000008.11:27178517:ACA:A	(self)
290826651, 19897130, 63436433, ss3721673318, ss3963519129, ss5729599329, ss5888255372	NC_000008.11:27178517:AC:	NC_000008.11:27178517:ACA:A	(self)
10546115457	NC_000008.11:27178517:ACA:A	NC_000008.11:27178517: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 rs1491465420

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

rs1491465420