rs2032624

Variant names:

• chrY-12914512-C-A
• rs2032624
• NM_004660.5:c.674-52C>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 23 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDX3Y	NM_004660.5	c.674-52C>A		intron_variant	Intron 7 of 16	ENST00000336079.8	NP_004651.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX3Y	ENST00000336079.8	c.674-52C>A		intron_variant	Intron 7 of 16	1	NM_004660.5	ENSP00000336725.3

Frequencies

GnomAD3 genomes AF: 0.600 AC: 19565 AN: 32611 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.960

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.566

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.482 AC: 118804 AN: 246397 Hom.: 0 Cov.: 0 AF XY: 0.482 AC XY: 118804 AN XY: 246397

African (AFR) AF: 0.847 AC: 4356 AN: 5141

American (AMR) AF: 0.590 AC: 4785 AN: 8115

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 4659 AN: 5785

East Asian (EAS) AF: 0.998 AC: 9042 AN: 9059

South Asian (SAS) AF: 0.644 AC: 17807 AN: 27632

European-Finnish (FIN) AF: 0.914 AC: 11578 AN: 12666

Middle Eastern (MID) AF: 0.905 AC: 1080 AN: 1194

European-Non Finnish (NFE) AF: 0.360 AC: 59844 AN: 166240

Other (OTH) AF: 0.535 AC: 5653 AN: 10565

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.601 AC: 19639 AN: 32675 Hom.: 0 Cov.: 0 AF XY: 0.601 AC XY: 19639 AN XY: 32675

African (AFR) AF: 0.800 AC: 6661 AN: 8327

American (AMR) AF: 0.506 AC: 1833 AN: 3626

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 614 AN: 755

East Asian (EAS) AF: 0.997 AC: 1252 AN: 1256

South Asian (SAS) AF: 0.657 AC: 968 AN: 1474

European-Finnish (FIN) AF: 0.939 AC: 3015 AN: 3211

Middle Eastern (MID) AF: 0.959 AC: 71 AN: 74

European-Non Finnish (NFE) AF: 0.369 AC: 4907 AN: 13289

Other (OTH) AF: 0.574 AC: 265 AN: 462

Alfa AF: 0.447 Hom.: 26299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
PhyloP100		0.070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2032624; hg19: chrY-15026424;