Genetic Variant DDX27:n.1545T>C (chr20-49235382-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000471144.1(DDX27):n.1545T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 296,202 control chromosomes in the GnomAD database, including 7,281 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4254 hom., cov: 32)

Exomes 𝑓: 0.20 ( 3027 hom. )

Consequence

DDX27
ENST00000471144.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Publications

15 publications found

Variant links:

Genes affected

DDX27 (HGNC:15837): (DEAD-box helicase 27) 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 involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. [provided by RefSeq, Jan 2017]

DDX27 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDX27	NM_017895.8 link	c.1427+294T>C		intron_variant	Intron 12 of 20	ENST00000618172.5	NP_060365.8
DDX27	NM_001348187.2 link	c.1520+294T>C		intron_variant	Intron 13 of 21		NP_001335116.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
DDX27	ENST00000471144.1 link	n.1545T>C	non_coding_transcript_exon_variant	Exon 1 of 7	1
DDX27	ENST00000484427.5 link	n.3048T>C	non_coding_transcript_exon_variant	Exon 11 of 19	1
DDX27	ENST00000618172.5 link	c.1427+294T>C	intron_variant	Intron 12 of 20	1	NM_017895.8	ENSP00000482680.1

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34711

AN:

151972

Hom.:

4248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.0520

Gnomad SAS

AF:

0.0872

Gnomad FIN

AF:

0.215

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.201

AC:

28929

AN:

144112

Hom.:

3027

Cov.:

AF XY:

0.198

AC XY:

14477

AN XY:

73114

show subpopulations

African (AFR)

AF:

0.310

AC:

1506

AN:

4860

American (AMR)

AF:

0.166

AC:

873

AN:

5248

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

1022

AN:

5692

East Asian (EAS)

AF:

0.0838

AC:

960

AN:

11450

South Asian (SAS)

AF:

0.0880

AC:

311

AN:

3534

European-Finnish (FIN)

AF:

0.209

AC:

2080

AN:

9940

Middle Eastern (MID)

AF:

0.152

AC:

118

AN:

776

European-Non Finnish (NFE)

AF:

0.217

AC:

20149

AN:

92818

Other (OTH)

AF:

0.195

AC:

1910

AN:

9794

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1104

2209

3313

4418

5522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.228

AC:

34750

AN:

152090

Hom.:

4254

Cov.:

AF XY:

0.223

AC XY:

16563

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.314

AC:

13008

AN:

41446

American (AMR)

AF:

0.175

AC:

2667

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

578

AN:

3468

East Asian (EAS)

AF:

0.0519

AC:

269

AN:

5184

South Asian (SAS)

AF:

0.0885

AC:

427

AN:

4826

European-Finnish (FIN)

AF:

0.215

AC:

2276

AN:

10590

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.218

AC:

14823

AN:

67982

Other (OTH)

AF:

0.181

AC:

382

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1337

2673

4010

5346

6683

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.212

Hom.:

2670

Bravo

AF:

0.226

Asia WGS

AF:

0.103

AC:

359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

(source)

DANN

Benign

0.58

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over