Variant 1-111766350-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007204.5(DDX20):c.1926G>A(p.Val642Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,613,552 control chromosomes in the GnomAD database, including 140,356 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 0.48 ( 19098 hom., cov: 32)

Exomes 𝑓: 0.40 ( 121258 hom. )

Consequence

DDX20
NM_007204.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

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:

DDX20 (HGNC:):

DDX20 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 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.1926G>A	p.Val642Val	synonymous_variant	11/11	ENST00000369702.5	NP_009135.4	Q9UHI6-1Q9H4N4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX20	ENST00000369702.5 linkuse as main transcript	c.1926G>A	p.Val642Val	synonymous_variant	11/11	1	NM_007204.5	ENSP00000358716.4		Q9UHI6-1

Frequencies

GnomAD3 genomes

AF:

0.483

AC:

73388

AN:

151986

Hom.:

19056

Cov.:

show subpopulations

Gnomad AFR

AF:

0.691

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.462

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.476

GnomAD3 exomes

AF:

0.427

AC:

107035

AN:

250932

Hom.:

23926

AF XY:

0.413

AC XY:

56094

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.699

Gnomad AMR exome

AF:

0.531

Gnomad ASJ exome

AF:

0.357

Gnomad EAS exome

AF:

0.345

Gnomad SAS exome

AF:

0.338

Gnomad FIN exome

AF:

0.451

Gnomad NFE exome

AF:

0.395

Gnomad OTH exome

AF:

0.411

GnomAD4 exome

AF:

0.402

AC:

587501

AN:

1461446

Hom.:

121258

Cov.:

AF XY:

0.399

AC XY:

289990

AN XY:

727038

show subpopulations

Gnomad4 AFR exome

AF:

0.710

Gnomad4 AMR exome

AF:

0.524

Gnomad4 ASJ exome

AF:

0.356

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.337

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.393

Gnomad4 OTH exome

AF:

0.404

GnomAD4 genome

AF:

0.483

AC:

73498

AN:

152106

Hom.:

19098

Cov.:

AF XY:

0.480

AC XY:

35657

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.692

Gnomad4 AMR

AF:

0.463

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.474

Alfa

AF:

0.400

Hom.:

21666

Bravo

AF:

0.496

Asia WGS

AF:

0.349

AC:

1221

AN:

3478

EpiCase

AF:

0.394

EpiControl

AF:

0.384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.12

DANN

Benign

0.52

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