Variant 1-111761169-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007204.5(DDX20):c.962+44A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 1,611,488 control chromosomes in the GnomAD database, including 1,458 homozygotes. 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 0.036 ( 133 hom., cov: 33)

Exomes 𝑓: 0.039 ( 1325 hom. )

Consequence

DDX20
NM_007204.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.525

Variant links:

Genes affected

DDX20 (HGNC:2743): (DEAD-box helicase 20) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which has an ATPase activity and is a component of the survival of motor neurons (SMN) complex. This protein interacts directly with SMN, the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on RNPs. [provided by RefSeq, Jul 2008]

DDX20 links:

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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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX20	NM_007204.5 linkuse as main transcript	c.962+44A>T		intron_variant		ENST00000369702.5	NP_009135.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX20	ENST00000369702.5 linkuse as main transcript	c.962+44A>T		intron_variant		1	NM_007204.5	ENSP00000358716	P2	Q9UHI6-1

Frequencies

GnomAD3 genomes

AF:

0.0356

AC:

5414

AN:

152218

Hom.:

131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0212

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0595

Gnomad ASJ

AF:

0.0438

Gnomad EAS

AF:

0.0724

Gnomad SAS

AF:

0.0300

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0372

Gnomad OTH

AF:

0.0392

GnomAD3 exomes

AF:

0.0477

AC:

11908

AN:

249606

Hom.:

399

AF XY:

0.0448

AC XY:

6051

AN XY:

134952

show subpopulations

Gnomad AFR exome

AF:

0.0180

Gnomad AMR exome

AF:

0.107

Gnomad ASJ exome

AF:

0.0457

Gnomad EAS exome

AF:

0.0743

Gnomad SAS exome

AF:

0.0273

Gnomad FIN exome

AF:

0.0332

Gnomad NFE exome

AF:

0.0379

Gnomad OTH exome

AF:

0.0532

GnomAD4 exome

AF:

0.0391

AC:

57034

AN:

1459152

Hom.:

1325

Cov.:

AF XY:

0.0385

AC XY:

27965

AN XY:

725804

show subpopulations

Gnomad4 AFR exome

AF:

0.0190

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.0479

Gnomad4 EAS exome

AF:

0.0780

Gnomad4 SAS exome

AF:

0.0279

Gnomad4 FIN exome

AF:

0.0346

Gnomad4 NFE exome

AF:

0.0365

Gnomad4 OTH exome

AF:

0.0412

GnomAD4 genome

AF:

0.0357

AC:

5431

AN:

152336

Hom.:

133

Cov.:

AF XY:

0.0350

AC XY:

2609

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0215

Gnomad4 AMR

AF:

0.0596

Gnomad4 ASJ

AF:

0.0438

Gnomad4 EAS

AF:

0.0728

Gnomad4 SAS

AF:

0.0306

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0372

Gnomad4 OTH

AF:

0.0383

Alfa

AF:

0.0380

Hom.:

Bravo

AF:

0.0391

Asia WGS

AF:

0.0510

AC:

179

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over