dbSNP rs2032590: DDX3Y:c.103+108T>G (chrY-12907702-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004660.5(DDX3Y):c.103+108T>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 0.059 ( 0 hom., 2007 hem., cov: 0)

Exomes 𝑓: 0.0089 ( 0 hom. 743 hem. )

Failed GnomAD Quality Control

Consequence

DDX3Y
NM_004660.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

7 publications found

Variant links:

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]

DDX3Y links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_004660.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004660.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DDX3Y	NM_004660.5	MANE Select	c.103+108T>G	intron	N/A	NP_004651.2
DDX3Y	NM_001122665.3		c.103+108T>G	intron	N/A	NP_001116137.1	O15523-1
DDX3Y	NM_001302552.3		c.94+108T>G	intron	N/A	NP_001289481.1	O15523-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DDX3Y	ENST00000336079.8	TSL:1 MANE Select	c.103+108T>G	intron	N/A	ENSP00000336725.3	O15523-1
DDX3Y	ENST00000360160.8	TSL:1	c.103+108T>G	intron	N/A	ENSP00000353284.4	O15523-1
DDX3Y	ENST00000894519.1		c.103+108T>G	intron	N/A	ENSP00000564578.1

Frequencies

GnomAD3 genomes

AF:

0.0587

AC:

1984

AN:

33790

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0103

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000644

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00102

Gnomad OTH

AF:

0.0390

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00895

AC:

743

AN:

83019

Hom.:

AF XY:

0.00895

AC XY:

743

AN XY:

83019

show subpopulations

African (AFR)

AF:

0.291

AC:

660

AN:

2267

American (AMR)

AF:

0.00508

AC:

AN:

2950

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2555

East Asian (EAS)

AF:

0.00

AC:

AN:

5881

South Asian (SAS)

AF:

0.00105

AC:

AN:

6673

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7410

Middle Eastern (MID)

AF:

0.00

AC:

AN:

383

European-Non Finnish (NFE)

AF:

0.000276

AC:

AN:

50691

Other (OTH)

AF:

0.0112

AC:

AN:

4209

Age Distribution

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0593

AC:

2007

AN:

33854

Hom.:

Cov.:

AF XY:

0.0593

AC XY:

2007

AN XY:

33854

show subpopulations

African (AFR)

AF:

0.227

AC:

1935

AN:

8524

American (AMR)

AF:

0.0103

AC:

AN:

3777

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

771

East Asian (EAS)

AF:

0.00

AC:

AN:

1332

South Asian (SAS)

AF:

0.000643

AC:

AN:

1556

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3470

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00102

AC:

AN:

13670

Other (OTH)

AF:

0.0387

AC:

AN:

465

Age Distribution

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0782

Hom.:

2163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

(source)

DANN

Benign

0.52

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over