Variant chr22-38486022-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006386.5(DDX17):c.2103G>A(p.Pro701Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 1,613,852 control chromosomes in the GnomAD database, including 317 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 153 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 164 hom. )

Consequence

DDX17
NM_006386.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.53

Variant links:

Genes affected

DDX17 (HGNC:2740): (DEAD-box helicase 17) 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 splicesosome 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 ATPase activated by a variety of RNA species, but not by dsDNA. This protein, and that encoded by DDX5 gene, are more closely related to each other than to any other member of the DEAD box family. This gene can encode multiple isoforms due to both alternative splicing and the use of alternative translation initiation codons, including a non-AUG (CUG) start codon. [provided by RefSeq, Apr 2011]

DDX17 links:

DDX17 (HGNC:):

DDX17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 22-38486022-C-T is Benign according to our data. Variant chr22-38486022-C-T is described in ClinVar as [Benign]. Clinvar id is 777708.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX17	NM_006386.5 linkuse as main transcript	c.2103G>A	p.Pro701Pro	synonymous_variant	13/13	ENST00000403230.3	NP_006377.2	Q92841-4
DDX17	NM_001098504.2 linkuse as main transcript	c.2109G>A	p.Pro703Pro	synonymous_variant	13/13		NP_001091974.1	A0A5H1ZRQ2Q59F66

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DDX17	ENST00000403230.3 linkuse as main transcript	c.2103G>A	p.Pro701Pro	synonymous_variant	13/13	1	NM_006386.5	ENSP00000385536.2	Q92841-4A0A1X7SBZ2
DDX17	ENST00000396821.8 linkuse as main transcript	c.2109G>A	p.Pro703Pro	synonymous_variant	13/13	1		ENSP00000380033.4	A0A5H1ZRQ2
DDX17	ENST00000216019.11 linkuse as main transcript	n.6100G>A		non_coding_transcript_exon_variant	12/12	1
DDX17	ENST00000431312.2 linkuse as main transcript	n.1508G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.0247

AC:

3752

AN:

151846

Hom.:

150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0862

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00873

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000279

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00646

AC:

1625

AN:

251472

Hom.:

AF XY:

0.00466

AC XY:

634

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.0885

Gnomad AMR exome

AF:

0.00327

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00109

Gnomad SAS exome

AF:

0.000261

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000290

Gnomad OTH exome

AF:

0.00212

GnomAD4 exome

AF:

0.00270

AC:

3948

AN:

1461888

Hom.:

164

Cov.:

AF XY:

0.00235

AC XY:

1712

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0894

Gnomad4 AMR exome

AF:

0.00456

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000428

Gnomad4 SAS exome

AF:

0.000174

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000338

Gnomad4 OTH exome

AF:

0.00518

GnomAD4 genome

AF:

0.0248

AC:

3762

AN:

151964

Hom.:

153

Cov.:

AF XY:

0.0239

AC XY:

1775

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.0862

Gnomad4 AMR

AF:

0.00872

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00136

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000280

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0107

Hom.:

Bravo

AF:

0.0285

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.000218

EpiControl

AF:

0.000356

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 21, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.24

DANN

Benign

0.69

Splicing

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