20-49235382-T-C

Variant names:

• chr20-49235382-T-C
• rs238150
• NM_017895.8:c.1427+294T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017895.8(DDX27):​c.1427+294T>C variant causes a intron 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 NM_017895.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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]

ACMG classification

Verdict is Benign. Variant got -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	c.1427+294T>C		intron_variant	Intron 12 of 20	ENST00000618172.5	NP_060365.8
DDX27	NM_001348187.2	c.1520+294T>C		intron_variant	Intron 13 of 21		NP_001335116.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34711 AN: 151972 Hom.: 4248 Cov.: 32

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.: 3 AF XY: 0.198 AC XY: 14477 AN XY: 73114

Gnomad4 AFR exome AF: 0.310

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.0838

Gnomad4 SAS exome AF: 0.0880

Gnomad4 FIN exome AF: 0.209

Gnomad4 NFE exome AF: 0.217

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.228 AC: 34750 AN: 152090 Hom.: 4254 Cov.: 32 AF XY: 0.223 AC XY: 16563 AN XY: 74392

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.181

Alfa AF: 0.210 Hom.: 1984

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
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs238150; hg19: chr20-47851919;