Variant 7-44569186-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_019082.4(DDX56):c.1237C>T(p.Leu413=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,613,972 control chromosomes in the GnomAD database, including 129 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 50 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 79 hom. )

Consequence

DDX56
NM_019082.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.27

Variant links:

Genes affected

DDX56 (HGNC:18193): (DEAD-box helicase 56) This gene encodes a member of the DEAD box protein family. 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. The protein encoded by this gene shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]

DDX56 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-44569186-G-A is Benign according to our data. Variant chr7-44569186-G-A is described in ClinVar as [Benign]. Clinvar id is 774873.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0164 (2506/152352) while in subpopulation AFR AF= 0.0444 (1846/41574). AF 95% confidence interval is 0.0427. There are 50 homozygotes in gnomad4. There are 1229 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 50 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX56	NM_019082.4 linkuse as main transcript	c.1237C>T	p.Leu413=	synonymous_variant	10/14	ENST00000258772.10	NP_061955.1
DDX56	NM_001257189.2 linkuse as main transcript	c.1117C>T	p.Leu373=	synonymous_variant	9/13		NP_001244118.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX56	ENST00000258772.10 linkuse as main transcript	c.1237C>T	p.Leu413=	synonymous_variant	10/14	1	NM_019082.4	ENSP00000258772	P1	Q9NY93-1

Frequencies

GnomAD3 genomes

AF:

0.0164

AC:

2503

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0444

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0207

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.00245

Gnomad OTH

AF:

0.0234

GnomAD3 exomes

AF:

0.00750

AC:

1882

AN:

251086

Hom.:

AF XY:

0.00624

AC XY:

847

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.0463

Gnomad AMR exome

AF:

0.0124

Gnomad ASJ exome

AF:

0.0243

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000490

Gnomad FIN exome

AF:

0.000278

Gnomad NFE exome

AF:

0.00322

Gnomad OTH exome

AF:

0.0116

GnomAD4 exome

AF:

0.00424

AC:

6196

AN:

1461620

Hom.:

Cov.:

AF XY:

0.00413

AC XY:

3005

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.0134

Gnomad4 ASJ exome

AF:

0.0220

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000557

Gnomad4 FIN exome

AF:

0.000281

Gnomad4 NFE exome

AF:

0.00227

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.0164

AC:

2506

AN:

152352

Hom.:

Cov.:

AF XY:

0.0165

AC XY:

1229

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.0444

Gnomad4 AMR

AF:

0.0207

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00245

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.00677

Hom.:

Bravo

AF:

0.0188

Asia WGS

AF:

0.00491

AC:

AN:

3478

EpiCase

AF:

0.00485

EpiControl

AF:

0.00433

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 11, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.21

Position offset: -15

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