Name: rs1491385580
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.

rs1491385580

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:168922161-168922164 (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: dupCACT
Variation Type: Indel Insertion and Deletion
Frequency: dupCACT=0.000014 (2/139368, GnomAD)
dupCACT=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CBR4 : Intron Variant
PALLD : 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	11862	CACT=1.00000	CACTCACT=0.00000	1.0	N/A
European	Sub	7618	CACT=1.0000	CACTCACT=0.0000	1.0	N/A
African	Sub	2816	CACT=1.0000	CACTCACT=0.0000	1.0	N/A
African Others	Sub	108	CACT=1.000	CACTCACT=0.000	1.0	N/A
African American	Sub	2708	CACT=1.0000	CACTCACT=0.0000	1.0	N/A
Asian	Sub	108	CACT=1.000	CACTCACT=0.000	1.0	N/A
East Asian	Sub	84	CACT=1.00	CACTCACT=0.00	1.0	N/A
Other Asian	Sub	24	CACT=1.00	CACTCACT=0.00	1.0	N/A
Latin American 1	Sub	146	CACT=1.000	CACTCACT=0.000	1.0	N/A
Latin American 2	Sub	610	CACT=1.000	CACTCACT=0.000	1.0	N/A
South Asian	Sub	94	CACT=1.00	CACTCACT=0.00	1.0	N/A
Other	Sub	470	CACT=1.000	CACTCACT=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
gnomAD - Genomes	Global	Study-wide	139368	- No frequency provided	dupCACT=0.000014
gnomAD - Genomes	European	Sub	75512	- No frequency provided	dupCACT=0.00000
gnomAD - Genomes	African	Sub	41726	- No frequency provided	dupCACT=0.00005
gnomAD - Genomes	American	Sub	13540	- No frequency provided	dupCACT=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	- No frequency provided	dupCACT=0.0000
gnomAD - Genomes	East Asian	Sub	3128	- No frequency provided	dupCACT=0.0000
gnomAD - Genomes	Other	Sub	2148	- No frequency provided	dupCACT=0.0000
Allele Frequency Aggregator	Total	Global	11862	CACT=1.00000	dupCACT=0.00000
Allele Frequency Aggregator	European	Sub	7618	CACT=1.0000	dupCACT=0.0000
Allele Frequency Aggregator	African	Sub	2816	CACT=1.0000	dupCACT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	CACT=1.000	dupCACT=0.000
Allele Frequency Aggregator	Other	Sub	470	CACT=1.000	dupCACT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CACT=1.000	dupCACT=0.000
Allele Frequency Aggregator	Asian	Sub	108	CACT=1.000	dupCACT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	CACT=1.00	dupCACT=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 4	NC_000004.12:g.168922161_168922164dup
GRCh37.p13 chr 4	NC_000004.11:g.169843312_169843315dup
PALLD RefSeqGene	NG_013376.1:g.430096_430099dup

Gene: PALLD, palladin, cytoskeletal associated protein (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PALLD transcript variant 1	NM_001166108.2:c.3058+420… NM_001166108.2:c.3058+420_3058+423dup	N/A	Intron Variant
PALLD transcript variant 3	NM_001166109.2:c.1861+420… NM_001166109.2:c.1861+420_1861+423dup	N/A	Intron Variant
PALLD transcript variant 4	NM_001166110.2:c.1546+420… NM_001166110.2:c.1546+420_1546+423dup	N/A	Intron Variant
PALLD transcript variant 5	NM_001367567.1:c.886+420_… NM_001367567.1:c.886+420_886+423dup	N/A	Intron Variant
PALLD transcript variant 6	NM_001367568.1:c.937+420_… NM_001367568.1:c.937+420_937+423dup	N/A	Intron Variant
PALLD transcript variant 7	NM_001367569.1:c.886+420_… NM_001367569.1:c.886+420_886+423dup	N/A	Intron Variant
PALLD transcript variant 8	NM_001367570.1:c.937+420_… NM_001367570.1:c.937+420_937+423dup	N/A	Intron Variant
PALLD transcript variant 2	NM_016081.4:c.3007+420_30… NM_016081.4:c.3007+420_3007+423dup	N/A	Intron Variant
PALLD transcript variant X1	XM_011531768.3:c.3934+420… XM_011531768.3:c.3934+420_3934+423dup	N/A	Intron Variant
PALLD transcript variant X2	XM_011531769.3:c.3883+420… XM_011531769.3:c.3883+420_3883+423dup	N/A	Intron Variant
PALLD transcript variant X5	XM_011531771.3:c.3661+420… XM_011531771.3:c.3661+420_3661+423dup	N/A	Intron Variant
PALLD transcript variant X6	XM_011531772.3:c.3562+420… XM_011531772.3:c.3562+420_3562+423dup	N/A	Intron Variant
PALLD transcript variant X7	XM_011531773.2:c.3262+420… XM_011531773.2:c.3262+420_3262+423dup	N/A	Intron Variant
PALLD transcript variant X8	XM_011531774.2:c.3211+420… XM_011531774.2:c.3211+420_3211+423dup	N/A	Intron Variant
PALLD transcript variant X10	XM_011531775.2:c.2584+420… XM_011531775.2:c.2584+420_2584+423dup	N/A	Intron Variant
PALLD transcript variant X11	XM_024453939.2:c.2584+420… XM_024453939.2:c.2584+420_2584+423dup	N/A	Intron Variant
PALLD transcript variant X15	XM_024453940.2:c.1597+420… XM_024453940.2:c.1597+420_1597+423dup	N/A	Intron Variant
PALLD transcript variant X3	XM_047449861.1:c.3934+420… XM_047449861.1:c.3934+420_3934+423dup	N/A	Intron Variant
PALLD transcript variant X4	XM_047449862.1:c.3883+420… XM_047449862.1:c.3883+420_3883+423dup	N/A	Intron Variant
PALLD transcript variant X9	XM_047449863.1:c.2890+420… XM_047449863.1:c.2890+420_2890+423dup	N/A	Intron Variant
PALLD transcript variant X12	XM_047449864.1:c.2584+420… XM_047449864.1:c.2584+420_2584+423dup	N/A	Intron Variant
PALLD transcript variant X13	XM_047449865.1:c.2533+420… XM_047449865.1:c.2533+420_2533+423dup	N/A	Intron Variant
PALLD transcript variant X14	XM_047449866.1:c.1861+420… XM_047449866.1:c.1861+420_1861+423dup	N/A	Intron Variant
PALLD transcript variant X16	XM_047449867.1:c.1324+420… XM_047449867.1:c.1324+420_1324+423dup	N/A	Intron Variant
PALLD transcript variant X17	XM_047449868.1:c.1225+420… XM_047449868.1:c.1225+420_1225+423dup	N/A	Intron Variant
PALLD transcript variant X18	XM_047449869.1:c.1324+420… XM_047449869.1:c.1324+420_1324+423dup	N/A	Intron Variant
PALLD transcript variant X19	XM_047449870.1:c.886+420_… XM_047449870.1:c.886+420_886+423dup	N/A	Intron Variant

Gene: CBR4, carbonyl reductase 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CBR4 transcript	NM_032783.5:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X3	XM_005263315.4:c.536-2739… XM_005263315.4:c.536-27399_536-27396dup	N/A	Intron Variant
CBR4 transcript variant X2	XM_017008782.2:c.566-2739… XM_017008782.2:c.566-27399_566-27396dup	N/A	Intron Variant
CBR4 transcript variant X1	XM_006714391.2:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X7	XM_011532385.2:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X9	XM_011532386.3:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X4	XM_017008783.3:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X8	XM_047416331.1:c.	N/A	Genic Downstream Transcript Variant
CBR4 transcript variant X5	XR_001741341.2:n.	N/A	Intron Variant
CBR4 transcript variant X6	XR_007057980.1: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	CACT=	dupCACT
GRCh38.p14 chr 4	NC_000004.12:g.168922161_168922164=	NC_000004.12:g.168922161_168922164dup
GRCh37.p13 chr 4	NC_000004.11:g.169843312_169843315=	NC_000004.11:g.169843312_169843315dup
PALLD RefSeqGene	NG_013376.1:g.430096_430099=	NG_013376.1:g.430096_430099dup
PALLD transcript variant 1	NM_001166108.1:c.3058+420=	NM_001166108.1:c.3058+420_3058+423dup
PALLD transcript variant 1	NM_001166108.2:c.3058+420=	NM_001166108.2:c.3058+420_3058+423dup
PALLD transcript variant 3	NM_001166109.1:c.1861+420=	NM_001166109.1:c.1861+420_1861+423dup
PALLD transcript variant 3	NM_001166109.2:c.1861+420=	NM_001166109.2:c.1861+420_1861+423dup
PALLD transcript variant 4	NM_001166110.1:c.1546+420=	NM_001166110.1:c.1546+420_1546+423dup
PALLD transcript variant 4	NM_001166110.2:c.1546+420=	NM_001166110.2:c.1546+420_1546+423dup
PALLD transcript variant 5	NM_001367567.1:c.886+420=	NM_001367567.1:c.886+420_886+423dup
PALLD transcript variant 6	NM_001367568.1:c.937+420=	NM_001367568.1:c.937+420_937+423dup
PALLD transcript variant 7	NM_001367569.1:c.886+420=	NM_001367569.1:c.886+420_886+423dup
PALLD transcript variant 8	NM_001367570.1:c.937+420=	NM_001367570.1:c.937+420_937+423dup
PALLD transcript variant 2	NM_016081.3:c.3007+420=	NM_016081.3:c.3007+420_3007+423dup
PALLD transcript variant 2	NM_016081.4:c.3007+420=	NM_016081.4:c.3007+420_3007+423dup
PALLD transcript variant X1	XM_005262861.1:c.3730+420=	XM_005262861.1:c.3730+420_3730+423dup
PALLD transcript variant X2	XM_005262862.1:c.3679+420=	XM_005262862.1:c.3679+420_3679+423dup
PALLD transcript variant X3	XM_005262863.1:c.3730+420=	XM_005262863.1:c.3730+420_3730+423dup
PALLD transcript variant X4	XM_005262864.1:c.3457+420=	XM_005262864.1:c.3457+420_3457+423dup
PALLD transcript variant X5	XM_005262865.1:c.3358+420=	XM_005262865.1:c.3358+420_3358+423dup
PALLD transcript variant X6	XM_005262866.1:c.2584+420=	XM_005262866.1:c.2584+420_2584+423dup
CBR4 transcript variant X2	XM_005263315.1:c.536-27396=	XM_005263315.1:c.536-27399_536-27396dup
CBR4 transcript variant X3	XM_005263315.4:c.536-27396=	XM_005263315.4:c.536-27399_536-27396dup
PALLD transcript variant X1	XM_011531768.3:c.3934+420=	XM_011531768.3:c.3934+420_3934+423dup
PALLD transcript variant X2	XM_011531769.3:c.3883+420=	XM_011531769.3:c.3883+420_3883+423dup
PALLD transcript variant X5	XM_011531771.3:c.3661+420=	XM_011531771.3:c.3661+420_3661+423dup
PALLD transcript variant X6	XM_011531772.3:c.3562+420=	XM_011531772.3:c.3562+420_3562+423dup
PALLD transcript variant X7	XM_011531773.2:c.3262+420=	XM_011531773.2:c.3262+420_3262+423dup
PALLD transcript variant X8	XM_011531774.2:c.3211+420=	XM_011531774.2:c.3211+420_3211+423dup
PALLD transcript variant X10	XM_011531775.2:c.2584+420=	XM_011531775.2:c.2584+420_2584+423dup
CBR4 transcript variant X2	XM_017008782.2:c.566-27396=	XM_017008782.2:c.566-27399_566-27396dup
PALLD transcript variant X11	XM_024453939.2:c.2584+420=	XM_024453939.2:c.2584+420_2584+423dup
PALLD transcript variant X15	XM_024453940.2:c.1597+420=	XM_024453940.2:c.1597+420_1597+423dup
PALLD transcript variant X3	XM_047449861.1:c.3934+420=	XM_047449861.1:c.3934+420_3934+423dup
PALLD transcript variant X4	XM_047449862.1:c.3883+420=	XM_047449862.1:c.3883+420_3883+423dup
PALLD transcript variant X9	XM_047449863.1:c.2890+420=	XM_047449863.1:c.2890+420_2890+423dup
PALLD transcript variant X12	XM_047449864.1:c.2584+420=	XM_047449864.1:c.2584+420_2584+423dup
PALLD transcript variant X13	XM_047449865.1:c.2533+420=	XM_047449865.1:c.2533+420_2533+423dup
PALLD transcript variant X14	XM_047449866.1:c.1861+420=	XM_047449866.1:c.1861+420_1861+423dup
PALLD transcript variant X16	XM_047449867.1:c.1324+420=	XM_047449867.1:c.1324+420_1324+423dup
PALLD transcript variant X17	XM_047449868.1:c.1225+420=	XM_047449868.1:c.1225+420_1225+423dup
PALLD transcript variant X18	XM_047449869.1:c.1324+420=	XM_047449869.1:c.1324+420_1324+423dup
PALLD transcript variant X19	XM_047449870.1:c.886+420=	XM_047449870.1:c.886+420_886+423dup

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#.

1 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2818403662	Jan 10, 2018 (151)
2	gnomAD - Genomes	NC_000004.12 - 168922161	Apr 26, 2021 (155)
3	ALFA	NC_000004.12 - 168922161	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
ss2818403662	NC_000004.11:169843311::CACT	NC_000004.12:168922160:CACT:CACTCA… NC_000004.12:168922160:CACT:CACTCACT	(self)
173007492	NC_000004.12:168922160::CACT	NC_000004.12:168922160:CACT:CACTCA… NC_000004.12:168922160:CACT:CACTCACT	(self)
8378161917	NC_000004.12:168922160:CACT:CACTCA… NC_000004.12:168922160:CACT:CACTCACT	NC_000004.12:168922160:CACT:CACTCA… NC_000004.12:168922160:CACT:CACTCACT	(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 rs1491385580

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491385580