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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.

rs1471887594

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:95533211-95533216 (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
delTCTG
Variation Type
Indel Insertion and Deletion
Frequency
delTCTG=0.000008 (2/251370, GnomAD_exome)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
USP44 : Frameshift Variant
Publications
0 citations
Genomic View
See rs on genome
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
gnomAD - Exomes Global Study-wide 251370 TGTCTG=0.999992 delTCTG=0.000008
gnomAD - Exomes European Sub 135332 TGTCTG=0.999993 delTCTG=0.000007
gnomAD - Exomes Asian Sub 49002 TGTCTG=1.00000 delTCTG=0.00000
gnomAD - Exomes American Sub 34574 TGTCTG=0.99997 delTCTG=0.00003
gnomAD - Exomes African Sub 16254 TGTCTG=1.00000 delTCTG=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 TGTCTG=1.00000 delTCTG=0.00000
gnomAD - Exomes Other Sub 6132 TGTCTG=1.0000 delTCTG=0.0000
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 12 NC_000012.12:g.95533213_95533216del
GRCh37.p13 chr 12 NC_000012.11:g.95926989_95926992del
USP44 RefSeqGene NG_052622.1:g.23316_23319del
Gene: USP44, ubiquitin specific peptidase 44 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
USP44 transcript variant 1 NM_032147.5:c.1043_1046del R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 NP_115523.2:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant 2 NM_001042403.3:c.1043_104…

NM_001042403.3:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 NP_001035862.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant 6 NM_001347937.2:c.1043_104…

NM_001347937.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 NP_001334866.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant 3 NM_001278393.2:c.1043_104…

NM_001278393.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 NP_001265322.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant 5 NM_001347936.2:c.1043_104…

NM_001347936.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 NP_001334865.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant 11 NR_144948.2:n.1390_1393del N/A Non Coding Transcript Variant
USP44 transcript variant 4 NR_125360.3:n.1199_1202del N/A Non Coding Transcript Variant
USP44 transcript variant 9 NR_144946.2:n.1145_1148del N/A Non Coding Transcript Variant
USP44 transcript variant 8 NR_144945.2:n.1145_1148del N/A Non Coding Transcript Variant
USP44 transcript variant 7 NR_144944.2:n.1390_1393del N/A Non Coding Transcript Variant
USP44 transcript variant 10 NR_144947.2:n.1145_1148del N/A Non Coding Transcript Variant
USP44 transcript variant X8 XM_011538803.1:c.1043_104…

XM_011538803.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537105.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X1 XM_005269172.2:c.1043_104…

XM_005269172.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269229.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X2 XM_011538804.3:c.1043_104…

XM_011538804.3:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537106.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X3 XM_005269174.2:c.1043_104…

XM_005269174.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269231.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X4 XM_011538802.2:c.1043_104…

XM_011538802.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537104.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X5 XM_011538800.3:c.1043_104…

XM_011538800.3:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537102.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X6 XM_011538801.2:c.1043_104…

XM_011538801.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537103.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X7 XM_005269173.2:c.1043_104…

XM_005269173.2:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269230.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X9 XM_011538805.3:c.1043_104…

XM_011538805.3:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537107.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X10 XM_047429642.1:c.1043_104…

XM_047429642.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285598.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X11 XM_047429643.1:c.1043_104…

XM_047429643.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285599.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X12 XM_047429644.1:c.1043_104…

XM_047429644.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285600.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X13 XM_047429645.1:c.1043_104…

XM_047429645.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285601.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X15 XM_011538806.3:c.1043_104…

XM_011538806.3:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X3 XP_011537108.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X16 XM_047429646.1:c.1043_104…

XM_047429646.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X4 XP_047285602.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X17 XM_047429647.1:c.1043_104…

XM_047429647.1:c.1043_1046del

R [AGA] > N [AA] Coding Sequence Variant
ubiquitin carboxyl-terminal hydrolase 44 isoform X4 XP_047285603.1:p.Arg348fs R (Arg) > N (Asn) Frameshift Variant
USP44 transcript variant X14 XR_944757.2:n.1318_1321del N/A Non Coding Transcript 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 TGTCTG= delTCTG
GRCh38.p14 chr 12 NC_000012.12:g.95533211_95533216= NC_000012.12:g.95533213_95533216del
GRCh37.p13 chr 12 NC_000012.11:g.95926987_95926992= NC_000012.11:g.95926989_95926992del
USP44 RefSeqGene NG_052622.1:g.23314_23319= NG_052622.1:g.23316_23319del
USP44 transcript variant 1 NM_032147.5:c.1041_1046= NM_032147.5:c.1043_1046del
USP44 transcript variant 1 NM_032147.4:c.1041_1046= NM_032147.4:c.1043_1046del
USP44 transcript variant 1 NM_032147.3:c.1041_1046= NM_032147.3:c.1043_1046del
USP44 transcript variant 2 NM_001042403.3:c.1041_1046= NM_001042403.3:c.1043_1046del
USP44 transcript variant 2 NM_001042403.2:c.1041_1046= NM_001042403.2:c.1043_1046del
USP44 transcript variant 4 NR_125360.3:n.1197_1202= NR_125360.3:n.1199_1202del
USP44 transcript variant 4 NR_125360.2:n.1239_1244= NR_125360.2:n.1241_1244del
USP44 transcript variant 4 NR_125360.1:n.1111_1116= NR_125360.1:n.1113_1116del
USP44 transcript variant 9 NR_144946.2:n.1143_1148= NR_144946.2:n.1145_1148del
USP44 transcript variant 9 NR_144946.1:n.1185_1190= NR_144946.1:n.1187_1190del
USP44 transcript variant 6 NM_001347937.2:c.1041_1046= NM_001347937.2:c.1043_1046del
USP44 transcript variant 6 NM_001347937.1:c.1041_1046= NM_001347937.1:c.1043_1046del
USP44 transcript variant 3 NM_001278393.2:c.1041_1046= NM_001278393.2:c.1043_1046del
USP44 transcript variant 3 NM_001278393.1:c.1041_1046= NM_001278393.1:c.1043_1046del
USP44 transcript variant 11 NR_144948.2:n.1388_1393= NR_144948.2:n.1390_1393del
USP44 transcript variant 11 NR_144948.1:n.1430_1435= NR_144948.1:n.1432_1435del
USP44 transcript variant 5 NM_001347936.2:c.1041_1046= NM_001347936.2:c.1043_1046del
USP44 transcript variant 5 NM_001347936.1:c.1041_1046= NM_001347936.1:c.1043_1046del
USP44 transcript variant 7 NR_144944.2:n.1388_1393= NR_144944.2:n.1390_1393del
USP44 transcript variant 7 NR_144944.1:n.1430_1435= NR_144944.1:n.1432_1435del
USP44 transcript variant 8 NR_144945.2:n.1143_1148= NR_144945.2:n.1145_1148del
USP44 transcript variant 8 NR_144945.1:n.1185_1190= NR_144945.1:n.1187_1190del
USP44 transcript variant 10 NR_144947.2:n.1143_1148= NR_144947.2:n.1145_1148del
USP44 transcript variant 10 NR_144947.1:n.1185_1190= NR_144947.1:n.1187_1190del
USP44 transcript variant X9 XM_011538805.3:c.1041_1046= XM_011538805.3:c.1043_1046del
USP44 transcript variant X9 XM_011538805.2:c.1041_1046= XM_011538805.2:c.1043_1046del
USP44 transcript variant X9 XM_011538805.1:c.1041_1046= XM_011538805.1:c.1043_1046del
USP44 transcript variant X2 XM_011538804.3:c.1041_1046= XM_011538804.3:c.1043_1046del
USP44 transcript variant X6 XM_011538804.2:c.1041_1046= XM_011538804.2:c.1043_1046del
USP44 transcript variant X8 XM_011538804.1:c.1041_1046= XM_011538804.1:c.1043_1046del
USP44 transcript variant X5 XM_011538800.3:c.1041_1046= XM_011538800.3:c.1043_1046del
USP44 transcript variant X5 XM_011538800.2:c.1041_1046= XM_011538800.2:c.1043_1046del
USP44 transcript variant X4 XM_011538800.1:c.1041_1046= XM_011538800.1:c.1043_1046del
USP44 transcript variant X15 XM_011538806.3:c.1041_1046= XM_011538806.3:c.1043_1046del
USP44 transcript variant X13 XM_011538806.2:c.1041_1046= XM_011538806.2:c.1043_1046del
USP44 transcript variant X11 XM_011538806.1:c.1041_1046= XM_011538806.1:c.1043_1046del
USP44 transcript variant X7 XM_005269173.2:c.1041_1046= XM_005269173.2:c.1043_1046del
USP44 transcript variant X3 XM_005269173.1:c.1041_1046= XM_005269173.1:c.1043_1046del
USP44 transcript variant X1 XM_005269172.2:c.1041_1046= XM_005269172.2:c.1043_1046del
USP44 transcript variant X1 XM_005269172.1:c.1041_1046= XM_005269172.1:c.1043_1046del
USP44 transcript variant X4 XM_011538802.2:c.1041_1046= XM_011538802.2:c.1043_1046del
USP44 transcript variant X7 XM_011538802.1:c.1041_1046= XM_011538802.1:c.1043_1046del
USP44 transcript variant X6 XM_011538801.2:c.1041_1046= XM_011538801.2:c.1043_1046del
USP44 transcript variant X4 XM_011538801.1:c.1041_1046= XM_011538801.1:c.1043_1046del
USP44 transcript variant X3 XM_005269174.2:c.1041_1046= XM_005269174.2:c.1043_1046del
USP44 transcript variant X2 XM_005269174.1:c.1041_1046= XM_005269174.1:c.1043_1046del
USP44 transcript variant X14 XR_944757.2:n.1316_1321= XR_944757.2:n.1318_1321del
USP44 transcript variant X11 XR_944757.1:n.1324_1329= XR_944757.1:n.1326_1329del
USP44 transcript variant X12 XM_047429644.1:c.1041_1046= XM_047429644.1:c.1043_1046del
USP44 transcript variant X11 XM_047429643.1:c.1041_1046= XM_047429643.1:c.1043_1046del
USP44 transcript variant X13 XM_047429645.1:c.1041_1046= XM_047429645.1:c.1043_1046del
USP44 transcript variant X8 XM_011538803.1:c.1041_1046= XM_011538803.1:c.1043_1046del
USP44 transcript variant X10 XM_047429642.1:c.1041_1046= XM_047429642.1:c.1043_1046del
USP44 transcript variant X16 XM_047429646.1:c.1041_1046= XM_047429646.1:c.1043_1046del
USP44 transcript variant X17 XM_047429647.1:c.1041_1046= XM_047429647.1:c.1043_1046del
ubiquitin carboxyl-terminal hydrolase 44 NP_115523.2:p.Ser347_Gln349= NP_115523.2:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 NP_001035862.1:p.Ser347_Gln349= NP_001035862.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 NP_001334866.1:p.Ser347_Gln349= NP_001334866.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 NP_001265322.1:p.Ser347_Gln349= NP_001265322.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 NP_001334865.1:p.Ser347_Gln349= NP_001334865.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537107.1:p.Ser347_Gln349= XP_011537107.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537106.1:p.Ser347_Gln349= XP_011537106.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537102.1:p.Ser347_Gln349= XP_011537102.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X3 XP_011537108.1:p.Ser347_Gln349= XP_011537108.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269230.1:p.Ser347_Gln349= XP_005269230.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269229.1:p.Ser347_Gln349= XP_005269229.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537104.1:p.Ser347_Gln349= XP_011537104.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537103.1:p.Ser347_Gln349= XP_011537103.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_005269231.1:p.Ser347_Gln349= XP_005269231.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285600.1:p.Ser347_Gln349= XP_047285600.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285599.1:p.Ser347_Gln349= XP_047285599.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285601.1:p.Ser347_Gln349= XP_047285601.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X1 XP_011537105.1:p.Ser347_Gln349= XP_011537105.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X2 XP_047285598.1:p.Ser347_Gln349= XP_047285598.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X4 XP_047285602.1:p.Ser347_Gln349= XP_047285602.1:p.Arg348fs
ubiquitin carboxyl-terminal hydrolase 44 isoform X4 XP_047285603.1:p.Ser347_Gln349= XP_047285603.1:p.Arg348fs
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#.

2 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2740042769 Nov 08, 2017 (151)
2 EVA ss5838369540 Oct 16, 2022 (156)
3 gnomAD - Exomes NC_000012.11 - 95926987 Jul 13, 2019 (153)
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
9278141, ss2740042769, ss5838369540 NC_000012.11:95926986:TGTC: NC_000012.12:95533210:TGTCTG:TG (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 rs1471887594

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