rs10189064
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_020935.3(USP37):c.2527+529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 152,128 control chromosomes in the GnomAD database, including 52 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 0.021 ( 52 hom., cov: 32)
Consequence
USP37
NM_020935.3 intron
NM_020935.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0860
Genes affected
USP37 (HGNC:20063): (ubiquitin specific peptidase 37) Enables cysteine-type endopeptidase activity; protein kinase binding activity; and thiol-dependent deubiquitinase. Involved in G1/S transition of mitotic cell cycle; protein deubiquitination; and regulation of DNA replication. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.84).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0207 (3154/152128) while in subpopulation NFE AF= 0.031 (2111/68006). AF 95% confidence interval is 0.0299. There are 52 homozygotes in gnomad4. There are 1379 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 3154 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP37 | NM_020935.3 | c.2527+529C>T | intron_variant | ENST00000258399.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP37 | ENST00000258399.8 | c.2527+529C>T | intron_variant | 1 | NM_020935.3 | P1 | |||
USP37 | ENST00000415516.5 | c.2245+529C>T | intron_variant | 1 | |||||
USP37 | ENST00000418019.5 | c.2527+529C>T | intron_variant | 1 | P1 | ||||
USP37 | ENST00000454775.5 | c.2527+529C>T | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0208 AC: 3155AN: 152010Hom.: 52 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0207 AC: 3154AN: 152128Hom.: 52 Cov.: 32 AF XY: 0.0185 AC XY: 1379AN XY: 74372
GnomAD4 genome
?
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152128
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32
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1379
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74372
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13
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at