Name: rs1471407557
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.

rs1471407557

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:121530758 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.00000 (0/14050, ALFA)
G=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLASP1-AS1 : Non Coding Transcript Variant
CLASP1 : Intron Variant
RNU4ATAC : 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	14050	A=1.00000	C=0.00000, G=0.00000	1.0	N/A
European	Sub	9690	A=1.0000	C=0.0000, G=0.0000	1.0	N/A
African	Sub	2898	A=1.0000	C=0.0000, G=0.0000	1.0	N/A
African Others	Sub	114	A=1.000	C=0.000, G=0.000	1.0	N/A
African American	Sub	2784	A=1.0000	C=0.0000, G=0.0000	1.0	N/A
Asian	Sub	112	A=1.000	C=0.000, G=0.000	1.0	N/A
East Asian	Sub	86	A=1.00	C=0.00, G=0.00	1.0	N/A
Other Asian	Sub	26	A=1.00	C=0.00, G=0.00	1.0	N/A
Latin American 1	Sub	146	A=1.000	C=0.000, G=0.000	1.0	N/A
Latin American 2	Sub	610	A=1.000	C=0.000, G=0.000	1.0	N/A
South Asian	Sub	98	A=1.00	C=0.00, G=0.00	1.0	N/A
Other	Sub	496	A=1.000	C=0.000, G=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	14050	A=1.00000	C=0.00000, G=0.00000
Allele Frequency Aggregator	European	Sub	9690	A=1.0000	C=0.0000, G=0.0000
Allele Frequency Aggregator	African	Sub	2898	A=1.0000	C=0.0000, G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Other	Sub	496	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	C=0.00, G=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.121530758A>C
GRCh38.p14 chr 2	NC_000002.12:g.121530758A>G
GRCh37.p13 chr 2	NC_000002.11:g.122288334A>C
GRCh37.p13 chr 2	NC_000002.11:g.122288334A>G
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.4879A>C
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.4879A>G

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.196-433T… NM_001142273.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 3	NM_001142274.2:c.196-433T… NM_001142274.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 4	NM_001207051.2:c.196-433T… NM_001207051.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 5	NM_001378003.1:c.196-433T… NM_001378003.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 6	NM_001378004.1:c.196-433T… NM_001378004.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 7	NM_001378005.1:c.196-433T… NM_001378005.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 8	NM_001395891.1:c.196-433T… NM_001395891.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant 1	NM_015282.3:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X15	XM_006712381.2:c.196-433T… XM_006712381.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X18	XM_006712382.2:c.196-433T… XM_006712382.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X21	XM_006712383.2:c.196-433T… XM_006712383.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X9	XM_011510848.2:c.196-433T… XM_011510848.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X10	XM_011510849.2:c.196-433T… XM_011510849.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X2	XM_017003665.2:c.196-433T… XM_017003665.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X12	XM_017003673.2:c.196-433T… XM_017003673.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X26	XM_017003690.2:c.196-433T… XM_017003690.2:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X1	XM_047443777.1:c.196-433T… XM_047443777.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X3	XM_047443778.1:c.196-433T… XM_047443778.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X4	XM_047443779.1:c.196-433T… XM_047443779.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X5	XM_047443780.1:c.196-433T… XM_047443780.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X6	XM_047443781.1:c.196-433T… XM_047443781.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X7	XM_047443782.1:c.196-433T… XM_047443782.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X8	XM_047443783.1:c.196-433T… XM_047443783.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X11	XM_047443784.1:c.196-433T… XM_047443784.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X13	XM_047443785.1:c.196-433T… XM_047443785.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X14	XM_047443786.1:c.196-433T… XM_047443786.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X16	XM_047443787.1:c.196-433T… XM_047443787.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X17	XM_047443788.1:c.196-433T… XM_047443788.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X19	XM_047443789.1:c.196-433T… XM_047443789.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X20	XM_047443791.1:c.196-433T… XM_047443791.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X22	XM_047443792.1:c.196-433T… XM_047443792.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X23	XM_047443793.1:c.196-433T… XM_047443793.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X25	XM_047443794.1:c.196-433T… XM_047443794.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X27	XM_047443795.1:c.196-433T… XM_047443795.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X28	XM_047443796.1:c.196-433T… XM_047443796.1:c.196-433T>G	N/A	Intron Variant
CLASP1 transcript variant X29	XM_047443797.1:c.196-433T… XM_047443797.1:c.196-433T>G	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) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RNU4ATAC transcript	NR_023343.1:n.	N/A	Upstream 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.591A>C	N/A	Non Coding Transcript Variant
CLASP1-AS1 transcript	XR_001739683.2:n.591A>G	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	A=	C	G
GRCh38.p14 chr 2	NC_000002.12:g.121530758=	NC_000002.12:g.121530758A>C	NC_000002.12:g.121530758A>G
GRCh37.p13 chr 2	NC_000002.11:g.122288334=	NC_000002.11:g.122288334A>C	NC_000002.11:g.122288334A>G
RNU4ATAC RefSeqGene (LRG_1202)	NG_029832.1:g.4879=	NG_029832.1:g.4879A>C	NG_029832.1:g.4879A>G
CLASP1-AS1 transcript	XR_001739683.2:n.591=	XR_001739683.2:n.591A>C	XR_001739683.2:n.591A>G
CLASP1-AS1 transcript	XR_001739683.1:n.427=	XR_001739683.1:n.427A>C	XR_001739683.1:n.427A>G
CLASP1 transcript variant 2	NM_001142273.1:c.196-433=	NM_001142273.1:c.196-433T>G	NM_001142273.1:c.196-433T>C
CLASP1 transcript variant 2	NM_001142273.2:c.196-433=	NM_001142273.2:c.196-433T>G	NM_001142273.2:c.196-433T>C
CLASP1 transcript variant 3	NM_001142274.1:c.196-433=	NM_001142274.1:c.196-433T>G	NM_001142274.1:c.196-433T>C
CLASP1 transcript variant 3	NM_001142274.2:c.196-433=	NM_001142274.2:c.196-433T>G	NM_001142274.2:c.196-433T>C
CLASP1 transcript variant 4	NM_001207051.1:c.196-433=	NM_001207051.1:c.196-433T>G	NM_001207051.1:c.196-433T>C
CLASP1 transcript variant 4	NM_001207051.2:c.196-433=	NM_001207051.2:c.196-433T>G	NM_001207051.2:c.196-433T>C
CLASP1 transcript variant 5	NM_001378003.1:c.196-433=	NM_001378003.1:c.196-433T>G	NM_001378003.1:c.196-433T>C
CLASP1 transcript variant 6	NM_001378004.1:c.196-433=	NM_001378004.1:c.196-433T>G	NM_001378004.1:c.196-433T>C
CLASP1 transcript variant 7	NM_001378005.1:c.196-433=	NM_001378005.1:c.196-433T>G	NM_001378005.1:c.196-433T>C
CLASP1 transcript variant 8	NM_001395891.1:c.196-433=	NM_001395891.1:c.196-433T>G	NM_001395891.1:c.196-433T>C
CLASP1 transcript variant 1	NM_015282.2:c.196-433=	NM_015282.2:c.196-433T>G	NM_015282.2:c.196-433T>C
CLASP1 transcript variant 1	NM_015282.3:c.196-433=	NM_015282.3:c.196-433T>G	NM_015282.3:c.196-433T>C
CLASP1 transcript variant X15	XM_006712381.2:c.196-433=	XM_006712381.2:c.196-433T>G	XM_006712381.2:c.196-433T>C
CLASP1 transcript variant X18	XM_006712382.2:c.196-433=	XM_006712382.2:c.196-433T>G	XM_006712382.2:c.196-433T>C
CLASP1 transcript variant X21	XM_006712383.2:c.196-433=	XM_006712383.2:c.196-433T>G	XM_006712383.2:c.196-433T>C
CLASP1 transcript variant X9	XM_011510848.2:c.196-433=	XM_011510848.2:c.196-433T>G	XM_011510848.2:c.196-433T>C
CLASP1 transcript variant X10	XM_011510849.2:c.196-433=	XM_011510849.2:c.196-433T>G	XM_011510849.2:c.196-433T>C
CLASP1 transcript variant X2	XM_017003665.2:c.196-433=	XM_017003665.2:c.196-433T>G	XM_017003665.2:c.196-433T>C
CLASP1 transcript variant X12	XM_017003673.2:c.196-433=	XM_017003673.2:c.196-433T>G	XM_017003673.2:c.196-433T>C
CLASP1 transcript variant X26	XM_017003690.2:c.196-433=	XM_017003690.2:c.196-433T>G	XM_017003690.2:c.196-433T>C
CLASP1 transcript variant X1	XM_047443777.1:c.196-433=	XM_047443777.1:c.196-433T>G	XM_047443777.1:c.196-433T>C
CLASP1 transcript variant X3	XM_047443778.1:c.196-433=	XM_047443778.1:c.196-433T>G	XM_047443778.1:c.196-433T>C
CLASP1 transcript variant X4	XM_047443779.1:c.196-433=	XM_047443779.1:c.196-433T>G	XM_047443779.1:c.196-433T>C
CLASP1 transcript variant X5	XM_047443780.1:c.196-433=	XM_047443780.1:c.196-433T>G	XM_047443780.1:c.196-433T>C
CLASP1 transcript variant X6	XM_047443781.1:c.196-433=	XM_047443781.1:c.196-433T>G	XM_047443781.1:c.196-433T>C
CLASP1 transcript variant X7	XM_047443782.1:c.196-433=	XM_047443782.1:c.196-433T>G	XM_047443782.1:c.196-433T>C
CLASP1 transcript variant X8	XM_047443783.1:c.196-433=	XM_047443783.1:c.196-433T>G	XM_047443783.1:c.196-433T>C
CLASP1 transcript variant X11	XM_047443784.1:c.196-433=	XM_047443784.1:c.196-433T>G	XM_047443784.1:c.196-433T>C
CLASP1 transcript variant X13	XM_047443785.1:c.196-433=	XM_047443785.1:c.196-433T>G	XM_047443785.1:c.196-433T>C
CLASP1 transcript variant X14	XM_047443786.1:c.196-433=	XM_047443786.1:c.196-433T>G	XM_047443786.1:c.196-433T>C
CLASP1 transcript variant X16	XM_047443787.1:c.196-433=	XM_047443787.1:c.196-433T>G	XM_047443787.1:c.196-433T>C
CLASP1 transcript variant X17	XM_047443788.1:c.196-433=	XM_047443788.1:c.196-433T>G	XM_047443788.1:c.196-433T>C
CLASP1 transcript variant X19	XM_047443789.1:c.196-433=	XM_047443789.1:c.196-433T>G	XM_047443789.1:c.196-433T>C
CLASP1 transcript variant X20	XM_047443791.1:c.196-433=	XM_047443791.1:c.196-433T>G	XM_047443791.1:c.196-433T>C
CLASP1 transcript variant X22	XM_047443792.1:c.196-433=	XM_047443792.1:c.196-433T>G	XM_047443792.1:c.196-433T>C
CLASP1 transcript variant X23	XM_047443793.1:c.196-433=	XM_047443793.1:c.196-433T>G	XM_047443793.1:c.196-433T>C
CLASP1 transcript variant X25	XM_047443794.1:c.196-433=	XM_047443794.1:c.196-433T>G	XM_047443794.1:c.196-433T>C
CLASP1 transcript variant X27	XM_047443795.1:c.196-433=	XM_047443795.1:c.196-433T>G	XM_047443795.1:c.196-433T>C
CLASP1 transcript variant X28	XM_047443796.1:c.196-433=	XM_047443796.1:c.196-433T>G	XM_047443796.1:c.196-433T>C
CLASP1 transcript variant X29	XM_047443797.1:c.196-433=	XM_047443797.1:c.196-433T>G	XM_047443797.1:c.196-433T>C

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#.

2 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TOPMED	ss4521586178	Apr 27, 2021 (155)
2	TOPMED	ss4521586179	Apr 27, 2021 (155)
3	TopMed Submission ignored due to conflicting rows: Row 325409057 (NC_000002.12:121530757:A:C 1/264690) Row 325409058 (NC_000002.12:121530757:A:G 1/264690)	-	Apr 27, 2021 (155)
4	TopMed Submission ignored due to conflicting rows: Row 325409057 (NC_000002.12:121530757:A:C 1/264690) Row 325409058 (NC_000002.12:121530757:A:G 1/264690)	-	Apr 27, 2021 (155)
5	ALFA	NC_000002.12 - 121530758	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
14938210938, ss4521586178	NC_000002.12:121530757:A:C	NC_000002.12:121530757:A:C	(self)
14938210938, ss4521586179	NC_000002.12:121530757:A:G	NC_000002.12:121530757:A:G	(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 rs1471407557

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

rs1471407557