22-38495934-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP6

The NM_006386.5(DDX17):ā€‹c.742C>Gā€‹(p.Leu248Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: not found (cov: 29)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DDX17
NM_006386.5 missense

Scores

2
8
9

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.32
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3407377).
BP6
Variant 22-38495934-G-C is Benign according to our data. Variant chr22-38495934-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2681230.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DDX17NM_006386.5 linkc.742C>G p.Leu248Val missense_variant 6/13 ENST00000403230.3 NP_006377.2 Q92841-4
DDX17NM_001098504.2 linkc.742C>G p.Leu248Val missense_variant 6/13 NP_001091974.1 A0A5H1ZRQ2Q59F66

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DDX17ENST00000403230.3 linkc.742C>G p.Leu248Val missense_variant 6/131 NM_006386.5 ENSP00000385536.2 Q92841-4A0A1X7SBZ2
DDX17ENST00000396821.8 linkc.742C>G p.Leu248Val missense_variant 6/131 ENSP00000380033.4 A0A5H1ZRQ2
DDX17ENST00000216019.11 linkn.799C>G non_coding_transcript_exon_variant 6/121
DDX17ENST00000432525.5 linkn.525C>G non_coding_transcript_exon_variant 6/122

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1375878
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
682738
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1
Likely benign, no assertion criteria providedresearchDepartment of Clinical Pathology, School of Medicine, Fujita Health University-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.55
BayesDel_addAF
Benign
-0.019
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.39
.;.;T;.
Eigen
Uncertain
0.19
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.97
.;D;D;D
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.34
T;T;T;T
MetaSVM
Benign
-1.2
T
MutationAssessor
Benign
1.4
.;.;L;.
PrimateAI
Pathogenic
0.86
D
PROVEAN
Uncertain
-2.9
D;D;.;.
REVEL
Benign
0.13
Sift
Uncertain
0.024
D;D;.;.
Sift4G
Uncertain
0.023
D;D;.;.
MVP
0.24
ClinPred
0.96
D
GERP RS
4.5
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.30
gMVP
0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-38891939; API