dbSNP rs2032636: DDX3Y:c.1020-13G>T (chrY-12915617-G-T) – 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.1020-13G>T 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 0.027 ( 0 hom., 897 hem., cov: 0)

Exomes 𝑓: 0.025 ( 0 hom. 8985 hem. )

Consequence

DDX3Y
NM_004660.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.70

Publications

21 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:

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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=-0.98).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0527 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.1020-13G>T	intron	N/A	NP_004651.2
DDX3Y	NM_001122665.3		c.1020-13G>T	intron	N/A	NP_001116137.1	O15523-1
DDX3Y	NM_001302552.3		c.1011-13G>T	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.1020-13G>T	intron	N/A	ENSP00000336725.3	O15523-1
DDX3Y	ENST00000360160.8	TSL:1	c.1020-13G>T	intron	N/A	ENSP00000353284.4	O15523-1
DDX3Y	ENST00000894519.1		c.1017-13G>T	intron	N/A	ENSP00000564578.1

Frequencies

GnomAD3 genomes

AF:

0.0269

AC:

894

AN:

33295

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00528

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.0593

Gnomad ASJ

AF:

0.0810

Gnomad EAS

AF:

0.000781

Gnomad SAS

AF:

0.0359

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.189

Gnomad NFE

AF:

0.0337

Gnomad OTH

AF:

0.0344

GnomAD4 exome

AF:

0.0249

AC:

8985

AN:

360127

Hom.:

Cov.:

AF XY:

0.0249

AC XY:

8985

AN XY:

360127

show subpopulations

African (AFR)

AF:

0.00499

AC:

AN:

7021

American (AMR)

AF:

0.0423

AC:

401

AN:

9482

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

681

AN:

6720

East Asian (EAS)

AF:

0.000106

AC:

AN:

9467

South Asian (SAS)

AF:

0.0305

AC:

977

AN:

31984

European-Finnish (FIN)

AF:

0.00163

AC:

AN:

12864

Middle Eastern (MID)

AF:

0.0647

AC:

105

AN:

1623

European-Non Finnish (NFE)

AF:

0.0236

AC:

6300

AN:

266776

Other (OTH)

AF:

0.0327

AC:

464

AN:

14190

Age Distribution

Exome Hom

Variant carriers

194

388

582

776

970

<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:

0.0269

AC:

897

AN:

33359

Hom.:

Cov.:

AF XY:

0.0269

AC XY:

897

AN XY:

33359

show subpopulations

African (AFR)

AF:

0.00525

AC:

AN:

8572

American (AMR)

AF:

0.0592

AC:

215

AN:

3631

Ashkenazi Jewish (ASJ)

AF:

0.0810

AC:

AN:

765

East Asian (EAS)

AF:

0.000781

AC:

AN:

1280

South Asian (SAS)

AF:

0.0365

AC:

AN:

1535

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3324

Middle Eastern (MID)

AF:

0.192

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0339

AC:

457

AN:

13495

Other (OTH)

AF:

0.0342

AC:

AN:

468

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:

0.0770

Hom.:

762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.041

(source)

PhyloP100

-4.7

Splicing

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