Variant rs2301659 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_019070.5(DDX49):c.853-78G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 1,498,574 control chromosomes in the GnomAD database, including 148,948 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 0.37 ( 12319 hom., cov: 32)

Exomes 𝑓: 0.44 ( 136629 hom. )

Consequence

DDX49
NM_019070.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.191

Variant links:

Genes affected

DDX49 (HGNC:18684): (DEAD-box helicase 49) Enables RNA binding activity. Involved in positive regulation of cell growth and regulation of rRNA stability. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DDX49 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
DDX49	NM_019070.5 linkuse as main transcript	c.853-78G>T	intron_variant	ENST00000247003.9
DDX49	XM_011528084.4 linkuse as main transcript	c.532-78G>T	intron_variant
DDX49	NR_033677.2 linkuse as main transcript	n.809-78G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX49	ENST00000247003.9 linkuse as main transcript	c.853-78G>T		intron_variant		1	NM_019070.5	P1	Q9Y6V7-1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

55955

AN:

151752

Hom.:

12313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.533

Gnomad ASJ

AF:

0.603

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.590

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.437

GnomAD4 exome

AF:

0.443

AC:

596386

AN:

1346704

Hom.:

136629

AF XY:

0.440

AC XY:

297505

AN XY:

675984

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.567

Gnomad4 ASJ exome

AF:

0.610

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.462

Gnomad4 OTH exome

AF:

0.427

GnomAD4 genome

AF:

0.369

AC:

55965

AN:

151870

Hom.:

12319

Cov.:

AF XY:

0.369

AC XY:

27370

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.533

Gnomad4 ASJ

AF:

0.603

Gnomad4 EAS

AF:

0.286

Gnomad4 SAS

AF:

0.291

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.465

Gnomad4 OTH

AF:

0.433

Alfa

AF:

0.427

Hom.:

3039

Bravo

AF:

0.372

Asia WGS

AF:

0.273

AC:

950

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

DANN

Benign

0.67

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