rs10158897
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003368.5(USP1):c.1250-93C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,205,848 control chromosomes in the GnomAD database, including 69,892 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.33 ( 8283 hom., cov: 33)
Exomes 𝑓: 0.34 ( 61609 hom. )
Consequence
USP1
NM_003368.5 intron
NM_003368.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.365
Genes affected
USP1 (HGNC:12607): (ubiquitin specific peptidase 1) This gene encodes a member of the ubiquitin-specific processing (UBP) family of proteases that is a deubiquitinating enzyme (DUB) with His and Cys domains. This protein is located in the cytoplasm and cleaves the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. The protein specifically deubiquitinates a protein in the Fanconi anemia (FA) DNA repair pathway. Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP1 | NM_003368.5 | c.1250-93C>T | intron_variant | ENST00000339950.5 | |||
USP1 | NM_001017415.2 | c.1250-93C>T | intron_variant | ||||
USP1 | NM_001017416.2 | c.1250-93C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP1 | ENST00000339950.5 | c.1250-93C>T | intron_variant | 1 | NM_003368.5 | P1 | |||
USP1 | ENST00000371146.5 | c.1250-93C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49723AN: 151948Hom.: 8274 Cov.: 33
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GnomAD4 exome AF: 0.336 AC: 354261AN: 1053782Hom.: 61609 AF XY: 0.339 AC XY: 177747AN XY: 525030
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GnomAD4 genome ? AF: 0.327 AC: 49757AN: 152066Hom.: 8283 Cov.: 33 AF XY: 0.326 AC XY: 24238AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at