Variant 1-200648405-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001031725.6(DDX59):c.1596+34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,607,978 control chromosomes in the GnomAD database, including 15,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1080 hom., cov: 31)

Exomes 𝑓: 0.13 ( 14356 hom. )

Consequence

DDX59
NM_001031725.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.813

Variant links:

Genes affected

DDX59 (HGNC:25360): (DEAD-box helicase 59) Predicted to enable RNA binding activity and RNA helicase activity. Predicted to be located in cytoplasm and nucleus. Predicted to be integral component of membrane. Implicated in orofaciodigital syndrome V. [provided by Alliance of Genome Resources, Apr 2022]

DDX59 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 1-200648405-G-T is Benign according to our data. Variant chr1-200648405-G-T is described in ClinVar as [Benign]. Clinvar id is 1269466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX59	NM_001031725.6 linkuse as main transcript	c.1596+34C>A		intron_variant		ENST00000331314.11	NP_001026895.2	Q5T1V6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX59	ENST00000331314.11 linkuse as main transcript	c.1596+34C>A		intron_variant		1	NM_001031725.6	ENSP00000330460.6		Q5T1V6-1

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15269

AN:

151950

Hom.:

1080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0263

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.0916

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0311

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.110

GnomAD3 exomes

AF:

0.103

AC:

25592

AN:

247414

Hom.:

1736

AF XY:

0.104

AC XY:

13855

AN XY:

133850

show subpopulations

Gnomad AFR exome

AF:

0.0225

Gnomad AMR exome

AF:

0.0655

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0345

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.134

AC:

195130

AN:

1455912

Hom.:

14356

Cov.:

AF XY:

0.131

AC XY:

94953

AN XY:

724154

show subpopulations

Gnomad4 AFR exome

AF:

0.0202

Gnomad4 AMR exome

AF:

0.0683

Gnomad4 ASJ exome

AF:

0.169

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0356

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.100

AC:

15266

AN:

152066

Hom.:

1080

Cov.:

AF XY:

0.0972

AC XY:

7224

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.0263

Gnomad4 AMR

AF:

0.0913

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0315

Gnomad4 FIN

AF:

0.131

Gnomad4 NFE

AF:

0.150

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.135

Hom.:

995

Bravo

AF:

0.0962

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.073

DANN

Benign

0.78

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over