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GeneBe

1-111762955-TATG-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_007204.5(DDX20):c.1268_1270del(p.Met423del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,613,950 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 18 hom. )

Consequence

DDX20
NM_007204.5 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.17
Variant links:
Genes affected
DDX20 (HGNC:2743): (DEAD-box helicase 20) 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. This gene encodes a DEAD box protein, which has an ATPase activity and is a component of the survival of motor neurons (SMN) complex. This protein interacts directly with SMN, the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on RNPs. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Nonframeshift variant in NON repetitive region in NM_007204.5. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-111762955-TATG-T is Benign according to our data. Variant chr1-111762955-TATG-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638995.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DDX20NM_007204.5 linkuse as main transcriptc.1268_1270del p.Met423del inframe_deletion 10/11 ENST00000369702.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DDX20ENST00000369702.5 linkuse as main transcriptc.1268_1270del p.Met423del inframe_deletion 10/111 NM_007204.5 P2Q9UHI6-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00261
AC:
397
AN:
152062
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000894
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000918
Gnomad ASJ
AF:
0.00404
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00472
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00407
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00235
AC:
590
AN:
251430
Hom.:
3
AF XY:
0.00249
AC XY:
339
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000665
Gnomad ASJ exome
AF:
0.00248
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000392
Gnomad FIN exome
AF:
0.00300
Gnomad NFE exome
AF:
0.00390
Gnomad OTH exome
AF:
0.00244
GnomAD4 exome
AF:
0.00345
AC:
5048
AN:
1461770
Hom.:
18
AF XY:
0.00338
AC XY:
2459
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.000448
Gnomad4 AMR exome
AF:
0.000760
Gnomad4 ASJ exome
AF:
0.00256
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000371
Gnomad4 FIN exome
AF:
0.00408
Gnomad4 NFE exome
AF:
0.00407
Gnomad4 OTH exome
AF:
0.00250
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00261
AC:
397
AN:
152180
Hom.:
1
Cov.:
32
AF XY:
0.00262
AC XY:
195
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.000891
Gnomad4 AMR
AF:
0.000916
Gnomad4 ASJ
AF:
0.00404
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00472
Gnomad4 NFE
AF:
0.00407
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000990
Hom.:
1
Bravo
AF:
0.00232
EpiCase
AF:
0.00398
EpiControl
AF:
0.00273

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023DDX20: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs538821511; hg19: chr1-112305577; API