9-132594789-C-G

Position:

• chr9-132594789-C-G

Variant summary

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

The NM_022779.9(DDX31):​c.*77G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 1,560,602 control chromosomes in the GnomAD database, including 462,168 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 0.81 (49807 hom., cov: 34)
  • Exomes 𝑓: 0.76 (412361 hom.)
• Consequence: DDX31 NM_022779.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

DDX31 (HGNC:16715): (DEAD-box helicase 31) 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 DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a member of this family. The function of this member has not been determined. Alternative splicing of this gene generates multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2016]

DDX31 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX31	NM_022779.9	c.*77G>C		3_prime_UTR_variant	20/20	ENST00000372159.8	NP_073616.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX31	ENST00000372159	c.*77G>C		3_prime_UTR_variant	20/20	1	NM_022779.9	ENSP00000361232.4
DDX31	ENST00000372155.2	n.551G>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122483 AN: 152152 Hom.: 49752 Cov.: 34

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.779

GnomAD4 exome AF: 0.764 AC: 1075968 AN: 1408332 Hom.: 412361 Cov.: 30 AF XY: 0.764 AC XY: 531107 AN XY: 695158

Gnomad4 AFR exome AF: 0.919

Gnomad4 AMR exome AF: 0.876

Gnomad4 ASJ exome AF: 0.754

Gnomad4 EAS exome AF: 0.668

Gnomad4 SAS exome AF: 0.785

Gnomad4 FIN exome AF: 0.720

Gnomad4 NFE exome AF: 0.760

Gnomad4 OTH exome AF: 0.772

GnomAD4 genome AF: 0.805 AC: 122596 AN: 152270 Hom.: 49807 Cov.: 34 AF XY: 0.803 AC XY: 59801 AN XY: 74448

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.776

Alfa AF: 0.701 Hom.: 2002

Bravo AF: 0.817

Asia WGS AF: 0.768 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.53

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: rs306549; hg19: chr9-135470176; COSMIC: COSV55037896; COSMIC: COSV55037896;