Name: rs1487164913
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.

rs1487164913

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:121531002-121531003 (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: delG / dupG
Variation Type: Indel Insertion and Deletion
Frequency: dupG=0.000014 (2/140168, GnomAD)
delG=0.00011 (3/28256, 14KJPN)
delG=0.00012 (2/16760, 8.3KJPN) (+ 2 more)
delG=0.00000 (0/10680, ALFA)
dupG=0.00000 (0/10680, ALFA)

Clinical Significance: Reported in ClinVar
Gene : Consequence: RNU4ATAC : Non Coding Transcript Variant
CLASP1 : Intron Variant
CLASP1-AS1 : 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	HWEP
Total	Global	10680	GG=1.00000	G=0.00000, GGG=0.00000	1.0	N/A
European	Sub	6962	GG=1.0000	G=0.0000, GGG=0.0000	1.0	N/A
African	Sub	2294	GG=1.0000	G=0.0000, GGG=0.0000	1.0	N/A
African Others	Sub	84	GG=1.00	G=0.00, GGG=0.00	1.0	N/A
African American	Sub	2210	GG=1.0000	G=0.0000, GGG=0.0000	1.0	N/A
Asian	Sub	108	GG=1.000	G=0.000, GGG=0.000	1.0	N/A
East Asian	Sub	84	GG=1.00	G=0.00, GGG=0.00	1.0	N/A
Other Asian	Sub	24	GG=1.00	G=0.00, GGG=0.00	1.0	N/A
Latin American 1	Sub	146	GG=1.000	G=0.000, GGG=0.000	1.0	N/A
Latin American 2	Sub	610	GG=1.000	G=0.000, GGG=0.000	1.0	N/A
South Asian	Sub	94	GG=1.00	G=0.00, GGG=0.00	1.0	N/A
Other	Sub	466	GG=1.000	G=0.000, GGG=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	140168	- No frequency provided	dupG=0.000014
gnomAD - Genomes	European	Sub	75924	- No frequency provided	dupG=0.00000
gnomAD - Genomes	African	Sub	42010	- No frequency provided	dupG=0.00002
gnomAD - Genomes	American	Sub	13632	- No frequency provided	dupG=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	- No frequency provided	dupG=0.0000
gnomAD - Genomes	East Asian	Sub	3128	- No frequency provided	dupG=0.0000
gnomAD - Genomes	Other	Sub	2152	- No frequency provided	dupG=0.0005
14KJPN	JAPANESE	Study-wide	28256	GG=0.99989	delG=0.00011
8.3KJPN	JAPANESE	Study-wide	16760	GG=0.99988	delG=0.00012
Allele Frequency Aggregator	Total	Global	10680	GG=1.00000	delG=0.00000, dupG=0.00000
Allele Frequency Aggregator	European	Sub	6962	GG=1.0000	delG=0.0000, dupG=0.0000
Allele Frequency Aggregator	African	Sub	2294	GG=1.0000	delG=0.0000, dupG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	GG=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Other	Sub	466	GG=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	GG=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Asian	Sub	108	GG=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	South Asian	Sub	94	GG=1.00	delG=0.00, dupG=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 2	NC_000002.12:g.121531003del
GRCh38.p14 chr 2	NC_000002.12:g.121531003dup
GRCh37.p13 chr 2	NC_000002.11:g.122288579del
GRCh37.p13 chr 2	NC_000002.11:g.122288579dup
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.5124del
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.5124dup

Gene: CLASP1, cytoplasmic linker associated protein 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLASP1 transcript variant 2	NM_001142273.2:c.196-677d… NM_001142273.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 3	NM_001142274.2:c.196-677d… NM_001142274.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 4	NM_001207051.2:c.196-677d… NM_001207051.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 5	NM_001378003.1:c.196-677d… NM_001378003.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 6	NM_001378004.1:c.196-677d… NM_001378004.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 7	NM_001378005.1:c.196-677d… NM_001378005.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 8	NM_001395891.1:c.196-677d… NM_001395891.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant 1	NM_015282.3:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X15	XM_006712381.2:c.196-677d… XM_006712381.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X18	XM_006712382.2:c.196-677d… XM_006712382.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X21	XM_006712383.2:c.196-677d… XM_006712383.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X9	XM_011510848.2:c.196-677d… XM_011510848.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X10	XM_011510849.2:c.196-677d… XM_011510849.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X2	XM_017003665.2:c.196-677d… XM_017003665.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X12	XM_017003673.2:c.196-677d… XM_017003673.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X26	XM_017003690.2:c.196-677d… XM_017003690.2:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X1	XM_047443777.1:c.196-677d… XM_047443777.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X3	XM_047443778.1:c.196-677d… XM_047443778.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X4	XM_047443779.1:c.196-677d… XM_047443779.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X5	XM_047443780.1:c.196-677d… XM_047443780.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X6	XM_047443781.1:c.196-677d… XM_047443781.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X7	XM_047443782.1:c.196-677d… XM_047443782.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X8	XM_047443783.1:c.196-677d… XM_047443783.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X11	XM_047443784.1:c.196-677d… XM_047443784.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X13	XM_047443785.1:c.196-677d… XM_047443785.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X14	XM_047443786.1:c.196-677d… XM_047443786.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X16	XM_047443787.1:c.196-677d… XM_047443787.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X17	XM_047443788.1:c.196-677d… XM_047443788.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X19	XM_047443789.1:c.196-677d… XM_047443789.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X20	XM_047443791.1:c.196-677d… XM_047443791.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X22	XM_047443792.1:c.196-677d… XM_047443792.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X23	XM_047443793.1:c.196-677d… XM_047443793.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X25	XM_047443794.1:c.196-677d… XM_047443794.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X27	XM_047443795.1:c.196-677d… XM_047443795.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X28	XM_047443796.1:c.196-677d… XM_047443796.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X29	XM_047443797.1:c.196-677d… XM_047443797.1:c.196-677del	N/A	Intron Variant
CLASP1 transcript variant X24	XM_017003682.3:c.	N/A	Genic Upstream Transcript Variant

Gene: RNU4ATAC, RNA, U4atac small nuclear (U12-dependent splicing) (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNU4ATAC transcript	NR_023343.1:n.124del	N/A	Non Coding Transcript Variant
RNU4ATAC transcript	NR_023343.1:n.124dup	N/A	Non Coding Transcript Variant

Gene: CLASP1-AS1, uncharacterized CLASP1-AS1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLASP1-AS1 transcript	XR_001739683.2: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.

Allele: delG (allele ID: 1214435 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001597535.2	not provided	Likely-Pathogenic

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	GG=	delG	dupG
GRCh38.p14 chr 2	NC_000002.12:g.121531002_121531003=	NC_000002.12:g.121531003del	NC_000002.12:g.121531003dup
GRCh37.p13 chr 2	NC_000002.11:g.122288578_122288579=	NC_000002.11:g.122288579del	NC_000002.11:g.122288579dup
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.5123_5124=	NG_029832.1:g.5124del	NG_029832.1:g.5124dup
RNU4ATAC transcript	NR_023343.1:n.123_124=	NR_023343.1:n.124del	NR_023343.1:n.124dup
CLASP1 transcript variant 2	NM_001142273.1:c.196-677=	NM_001142273.1:c.196-677del	NM_001142273.1:c.196-677dup
CLASP1 transcript variant 2	NM_001142273.2:c.196-677=	NM_001142273.2:c.196-677del	NM_001142273.2:c.196-677dup
CLASP1 transcript variant 3	NM_001142274.1:c.196-677=	NM_001142274.1:c.196-677del	NM_001142274.1:c.196-677dup
CLASP1 transcript variant 3	NM_001142274.2:c.196-677=	NM_001142274.2:c.196-677del	NM_001142274.2:c.196-677dup
CLASP1 transcript variant 4	NM_001207051.1:c.196-677=	NM_001207051.1:c.196-677del	NM_001207051.1:c.196-677dup
CLASP1 transcript variant 4	NM_001207051.2:c.196-677=	NM_001207051.2:c.196-677del	NM_001207051.2:c.196-677dup
CLASP1 transcript variant 5	NM_001378003.1:c.196-677=	NM_001378003.1:c.196-677del	NM_001378003.1:c.196-677dup
CLASP1 transcript variant 6	NM_001378004.1:c.196-677=	NM_001378004.1:c.196-677del	NM_001378004.1:c.196-677dup
CLASP1 transcript variant 7	NM_001378005.1:c.196-677=	NM_001378005.1:c.196-677del	NM_001378005.1:c.196-677dup
CLASP1 transcript variant 8	NM_001395891.1:c.196-677=	NM_001395891.1:c.196-677del	NM_001395891.1:c.196-677dup
CLASP1 transcript variant 1	NM_015282.2:c.196-677=	NM_015282.2:c.196-677del	NM_015282.2:c.196-677dup
CLASP1 transcript variant 1	NM_015282.3:c.196-677=	NM_015282.3:c.196-677del	NM_015282.3:c.196-677dup
CLASP1 transcript variant X15	XM_006712381.2:c.196-677=	XM_006712381.2:c.196-677del	XM_006712381.2:c.196-677dup
CLASP1 transcript variant X18	XM_006712382.2:c.196-677=	XM_006712382.2:c.196-677del	XM_006712382.2:c.196-677dup
CLASP1 transcript variant X21	XM_006712383.2:c.196-677=	XM_006712383.2:c.196-677del	XM_006712383.2:c.196-677dup
CLASP1 transcript variant X9	XM_011510848.2:c.196-677=	XM_011510848.2:c.196-677del	XM_011510848.2:c.196-677dup
CLASP1 transcript variant X10	XM_011510849.2:c.196-677=	XM_011510849.2:c.196-677del	XM_011510849.2:c.196-677dup
CLASP1 transcript variant X2	XM_017003665.2:c.196-677=	XM_017003665.2:c.196-677del	XM_017003665.2:c.196-677dup
CLASP1 transcript variant X12	XM_017003673.2:c.196-677=	XM_017003673.2:c.196-677del	XM_017003673.2:c.196-677dup
CLASP1 transcript variant X26	XM_017003690.2:c.196-677=	XM_017003690.2:c.196-677del	XM_017003690.2:c.196-677dup
CLASP1 transcript variant X1	XM_047443777.1:c.196-677=	XM_047443777.1:c.196-677del	XM_047443777.1:c.196-677dup
CLASP1 transcript variant X3	XM_047443778.1:c.196-677=	XM_047443778.1:c.196-677del	XM_047443778.1:c.196-677dup
CLASP1 transcript variant X4	XM_047443779.1:c.196-677=	XM_047443779.1:c.196-677del	XM_047443779.1:c.196-677dup
CLASP1 transcript variant X5	XM_047443780.1:c.196-677=	XM_047443780.1:c.196-677del	XM_047443780.1:c.196-677dup
CLASP1 transcript variant X6	XM_047443781.1:c.196-677=	XM_047443781.1:c.196-677del	XM_047443781.1:c.196-677dup
CLASP1 transcript variant X7	XM_047443782.1:c.196-677=	XM_047443782.1:c.196-677del	XM_047443782.1:c.196-677dup
CLASP1 transcript variant X8	XM_047443783.1:c.196-677=	XM_047443783.1:c.196-677del	XM_047443783.1:c.196-677dup
CLASP1 transcript variant X11	XM_047443784.1:c.196-677=	XM_047443784.1:c.196-677del	XM_047443784.1:c.196-677dup
CLASP1 transcript variant X13	XM_047443785.1:c.196-677=	XM_047443785.1:c.196-677del	XM_047443785.1:c.196-677dup
CLASP1 transcript variant X14	XM_047443786.1:c.196-677=	XM_047443786.1:c.196-677del	XM_047443786.1:c.196-677dup
CLASP1 transcript variant X16	XM_047443787.1:c.196-677=	XM_047443787.1:c.196-677del	XM_047443787.1:c.196-677dup
CLASP1 transcript variant X17	XM_047443788.1:c.196-677=	XM_047443788.1:c.196-677del	XM_047443788.1:c.196-677dup
CLASP1 transcript variant X19	XM_047443789.1:c.196-677=	XM_047443789.1:c.196-677del	XM_047443789.1:c.196-677dup
CLASP1 transcript variant X20	XM_047443791.1:c.196-677=	XM_047443791.1:c.196-677del	XM_047443791.1:c.196-677dup
CLASP1 transcript variant X22	XM_047443792.1:c.196-677=	XM_047443792.1:c.196-677del	XM_047443792.1:c.196-677dup
CLASP1 transcript variant X23	XM_047443793.1:c.196-677=	XM_047443793.1:c.196-677del	XM_047443793.1:c.196-677dup
CLASP1 transcript variant X25	XM_047443794.1:c.196-677=	XM_047443794.1:c.196-677del	XM_047443794.1:c.196-677dup
CLASP1 transcript variant X27	XM_047443795.1:c.196-677=	XM_047443795.1:c.196-677del	XM_047443795.1:c.196-677dup
CLASP1 transcript variant X28	XM_047443796.1:c.196-677=	XM_047443796.1:c.196-677del	XM_047443796.1:c.196-677dup
CLASP1 transcript variant X29	XM_047443797.1:c.196-677=	XM_047443797.1:c.196-677del	XM_047443797.1:c.196-677dup

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, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2746768564	Nov 08, 2017 (151)
2	GNOMAD	ss2778850404	Nov 08, 2017 (151)
3	TOMMO_GENOMICS	ss5153539155	Apr 27, 2021 (155)
4	TOMMO_GENOMICS	ss5683565180	Oct 12, 2022 (156)
5	gnomAD - Genomes	NC_000002.12 - 121531002	Apr 27, 2021 (155)
6	8.3KJPN	NC_000002.11 - 122288578	Apr 27, 2021 (155)
7	14KJPN	NC_000002.12 - 121531002	Oct 12, 2022 (156)
8	ALFA	NC_000002.12 - 121531002	Apr 27, 2021 (155)
9	ClinVar	RCV001597535.2	Oct 12, 2022 (156)

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
11508462, ss5153539155	NC_000002.11:122288577:G:	NC_000002.12:121531001:GG:G	(self)
17402284, ss5683565180	NC_000002.12:121531001:G:	NC_000002.12:121531001:GG:G
RCV001597535.2, 6519808897	NC_000002.12:121531001:GG:G	NC_000002.12:121531001:GG:G	(self)
ss2746768564, ss2778850404	NC_000002.11:122288577::G	NC_000002.12:121531001:GG:GGG	(self)
71769585	NC_000002.12:121531001::G	NC_000002.12:121531001:GG:GGG	(self)
6519808897	NC_000002.12:121531001:GG:GGG	NC_000002.12:121531001:GG:GGG	(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 rs1487164913

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

rs1487164913