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dbSNP Short Genetic Variations

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.

rs1481746960

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:129109496-129109497 (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
delAA
Variation Type
Deletion
Frequency
delAA=0.000008 (2/264690, TOPMED)
delAA=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C4orf33 : Frameshift 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 Alt HMOZ HTRZ HWEP
Total Global 14050 AA=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 9690 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2898 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 AA=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2784 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 AA=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AA=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AA=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 496 AA=1.000 =0.000 1.0 0.0 0.0 N/A


Help

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
TopMed Global Study-wide 264690 AA=0.999992 delAA=0.000008
Allele Frequency Aggregator Total Global 14050 AA=1.00000 delAA=0.00000
Allele Frequency Aggregator European Sub 9690 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator African Sub 2898 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AA=1.000 delAA=0.000
Allele Frequency Aggregator Other Sub 496 AA=1.000 delAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AA=1.000 delAA=0.000
Allele Frequency Aggregator Asian Sub 112 AA=1.000 delAA=0.000
Allele Frequency Aggregator South Asian Sub 98 AA=1.00 delAA=0.00
Help

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.129109496_129109497del
GRCh37.p13 chr 4 NC_000004.11:g.130030651_130030652del
Gene: C4orf33, chromosome 4 open reading frame 33 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
C4orf33 transcript variant 2 NM_001099783.2:c.318_319d…

NM_001099783.2:c.318_319del

R [AGAAT] > S [AGTG] Coding Sequence Variant
UPF0462 protein C4orf33 NP_001093253.1:p.Arg106fs R (Arg) > S (Ser) Frameshift Variant
C4orf33 transcript variant 1 NM_173487.3:c.318_319del R [AGAAT] > S [AGTG] Coding Sequence Variant
UPF0462 protein C4orf33 NP_775758.2:p.Arg106fs R (Arg) > S (Ser) Frameshift Variant
C4orf33 transcript variant X1 XM_047449598.1:c.318_319d…

XM_047449598.1:c.318_319del

R [AGAAT] > S [AGTG] Coding Sequence Variant
UPF0462 protein C4orf33 isoform X1 XP_047305554.1:p.Arg106fs R (Arg) > S (Ser) Frameshift Variant
C4orf33 transcript variant X2 XM_047449599.1:c.318_319d…

XM_047449599.1:c.318_319del

R [AGAAT] > S [AGTG] Coding Sequence Variant
UPF0462 protein C4orf33 isoform X2 XP_047305555.1:p.Arg106fs R (Arg) > S (Ser) Frameshift Variant
C4orf33 transcript variant X3 XM_017007724.2:c.318_319d…

XM_017007724.2:c.318_319del

R [AGAAT] > S [AGTG] Coding Sequence Variant
UPF0462 protein C4orf33 isoform X1 XP_016863213.1:p.Arg106fs R (Arg) > S (Ser) Frameshift Variant
Help

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
Help

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 AA= delAA
GRCh38.p14 chr 4 NC_000004.12:g.129109496_129109497= NC_000004.12:g.129109496_129109497del
GRCh37.p13 chr 4 NC_000004.11:g.130030651_130030652= NC_000004.11:g.130030651_130030652del
C4orf33 transcript variant 1 NM_173487.3:c.318_319= NM_173487.3:c.318_319del
C4orf33 transcript variant 1 NM_173487.2:c.318_319= NM_173487.2:c.318_319del
C4orf33 transcript variant 2 NM_001099783.2:c.318_319= NM_001099783.2:c.318_319del
C4orf33 transcript variant 2 NM_001099783.1:c.318_319= NM_001099783.1:c.318_319del
C4orf33 transcript variant X3 XM_017007724.2:c.318_319= XM_017007724.2:c.318_319del
C4orf33 transcript variant X4 XM_017007724.1:c.318_319= XM_017007724.1:c.318_319del
C4orf33 transcript variant X1 XM_047449598.1:c.318_319= XM_047449598.1:c.318_319del
C4orf33 transcript variant X2 XM_047449599.1:c.318_319= XM_047449599.1:c.318_319del
UPF0462 protein C4orf33 NP_775758.2:p.Arg106_Met107= NP_775758.2:p.Arg106fs
UPF0462 protein C4orf33 NP_001093253.1:p.Arg106_Met107= NP_001093253.1:p.Arg106fs
UPF0462 protein C4orf33 isoform X1 XP_016863213.1:p.Arg106_Met107= XP_016863213.1:p.Arg106fs
UPF0462 protein C4orf33 isoform X1 XP_047305554.1:p.Arg106_Met107= XP_047305554.1:p.Arg106fs
UPF0462 protein C4orf33 isoform X2 XP_047305555.1:p.Arg106_Met107= XP_047305555.1:p.Arg106fs
Help

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 TOPMED ss4631813732 Apr 26, 2021 (155)
2 TopMed NC_000004.12 - 129109496 Apr 26, 2021 (155)
3 ALFA NC_000004.12 - 129109496 Apr 26, 2021 (155)
Help

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
469191288, 3730819802, ss4631813732 NC_000004.12:129109495:AA: NC_000004.12:129109495:AA: (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1481746960

Help

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.

Software version is: 2.0.1.post820+afb47a3d