rs2032604
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004654.4(USP9Y):c.7530+48T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.035 ( 0 hom., 1162 hem., cov: 0)
Exomes 𝑓: 0.055 ( 0 hom. 12696 hem. )
Consequence
USP9Y
NM_004654.4 intron
NM_004654.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
Genes affected
USP9Y (HGNC:12633): (ubiquitin specific peptidase 9 Y-linked) This gene is a member of the peptidase C19 family. It encodes a protein that is similar to ubiquitin-specific proteases, which cleave the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. [provided by RefSeq, Mar 2009]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP9Y | NM_004654.4 | c.7530+48T>G | intron_variant | ENST00000338981.7 | |||
USP9Y | XM_047442771.1 | c.7296+48T>G | intron_variant | ||||
USP9Y | XM_047442772.1 | c.7530+48T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP9Y | ENST00000338981.7 | c.7530+48T>G | intron_variant | 1 | NM_004654.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0348 AC: 1163AN: 33437Hom.: 0 Cov.: 0 AF XY: 0.0348 AC XY: 1163AN XY: 33437
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GnomAD3 exomes AF: 0.0666 AC: 2568AN: 38542Hom.: 0 AF XY: 0.0666 AC XY: 2568AN XY: 38542
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GnomAD4 exome AF: 0.0550 AC: 12696AN: 230744Hom.: 0 Cov.: 0 AF XY: 0.0550 AC XY: 12696AN XY: 230744
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GnomAD4 genome ? AF: 0.0347 AC: 1162AN: 33496Hom.: 0 Cov.: 0 AF XY: 0.0347 AC XY: 1162AN XY: 33496
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ClinVar
Not reported inComputational scores
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Name
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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