Variant chr12-31092807-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_030653.4(DDX11):c.1243-39A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,575,780 control chromosomes in the GnomAD database, including 189,227 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 0.54 ( 23194 hom., cov: 32)

Exomes 𝑓: 0.47 ( 166033 hom. )

Consequence

DDX11
NM_030653.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Variant links:

Genes affected

DDX11 (HGNC:2736): (DEAD/H-box helicase 11) 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 is an enzyme that possesses both ATPase and DNA helicase activities. This gene is a homolog of the yeast CHL1 gene, and may function to maintain chromosome transmission fidelity and genome stability. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

DDX11 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX11	NM_030653.4 link	c.1243-39A>G		intron_variant		ENST00000542838.6	NP_085911.2	Q2NKM7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX11	ENST00000542838.6 link	c.1243-39A>G		intron_variant		1	NM_030653.4	ENSP00000443426.1		Q96FC9-2

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81573

AN:

151726

Hom.:

23140

Cov.:

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.457

Gnomad AMR

AF:

0.595

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.818

Gnomad SAS

AF:

0.570

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.444

Gnomad OTH

AF:

0.519

GnomAD3 exomes

AF:

0.527

AC:

131374

AN:

249468

Hom.:

36832

AF XY:

0.517

AC XY:

69823

AN XY:

135070

show subpopulations

Gnomad AFR exome

AF:

0.690

Gnomad AMR exome

AF:

0.662

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.811

Gnomad SAS exome

AF:

0.569

Gnomad FIN exome

AF:

0.414

Gnomad NFE exome

AF:

0.439

Gnomad OTH exome

AF:

0.494

GnomAD4 exome

AF:

0.472

AC:

672568

AN:

1423938

Hom.:

166033

Cov.:

AF XY:

0.474

AC XY:

336085

AN XY:

709584

show subpopulations

Gnomad4 AFR exome

AF:

0.680

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.401

Gnomad4 EAS exome

AF:

0.848

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.441

Gnomad4 OTH exome

AF:

0.492

GnomAD4 genome

AF:

0.538

AC:

81682

AN:

151842

Hom.:

23194

Cov.:

AF XY:

0.540

AC XY:

40083

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.679

Gnomad4 AMR

AF:

0.596

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.819

Gnomad4 SAS

AF:

0.570

Gnomad4 FIN

AF:

0.417

Gnomad4 NFE

AF:

0.444

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.475

Hom.:

3210

Bravo

AF:

0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.59

DANN

Benign

0.54

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