rs2032624
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004660.5(DDX3Y):c.674-52C>A 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 0.60 ( 0 hom., 19639 hem., cov: 0)
Exomes 𝑓: 0.48 ( 0 hom. 118804 hem. )
Failed GnomAD Quality Control
Consequence
DDX3Y
NM_004660.5 intron
NM_004660.5 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0700
Genes affected
DDX3Y (HGNC:2699): (DEAD-box helicase 3 Y-linked) The protein encoded by this gene is a member of the DEAD-box RNA helicase family, characterized by nine conserved motifs, included the conserved Asp-Glu-Ala-Asp (DEAD) motif. These motifs are thought to be involved in ATP binding, hydrolysis, RNA binding, and in the formation of intramolecular interactions. This protein shares high similarity to DDX3X, on the X chromosome, but a deletion of this gene is not complemented by DDX3X. Mutations in this gene result in male infertility, a reduction in germ cell numbers, and can result in Sertoli-cell only sydrome. Pseudogenes sharing similarity to both this gene and the DDX3X paralog are found on chromosome 4 and the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX3Y | NM_004660.5 | c.674-52C>A | intron_variant | ENST00000336079.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX3Y | ENST00000336079.8 | c.674-52C>A | intron_variant | 1 | NM_004660.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 19565AN: 32611Hom.: 0 Cov.: 0 AF XY: 0.600 AC XY: 19565AN XY: 32611 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.482 AC: 118804AN: 246397Hom.: 0 Cov.: 0 AF XY: 0.482 AC XY: 118804AN XY: 246397
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.601 AC: 19639AN: 32675Hom.: 0 Cov.: 0 AF XY: 0.601 AC XY: 19639AN XY: 32675
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at