9-132594789-C-G

Variant names:

• chr9-132594789-C-G
• rs306549
• NM_022779.9:c.*77G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022779.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX31	NM_022779.9	MANE Select	c.*77G>C		3_prime_UTR	Exon 20 of 20	NP_073616.7
	DDX31	NM_001322341.2		c.*77G>C		3_prime_UTR	Exon 21 of 21	NP_001309270.1
	DDX31	NM_001322343.1		c.*77G>C		3_prime_UTR	Exon 20 of 20	NP_001309272.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX31	ENST00000372159.8	TSL:1 MANE Select	c.*77G>C		3_prime_UTR	Exon 20 of 20	ENSP00000361232.4	Q9H8H2-5
	DDX31	ENST00000893393.1		c.*77G>C		3_prime_UTR	Exon 21 of 21	ENSP00000563452.1
	DDX31	ENST00000893392.1		c.*77G>C		3_prime_UTR	Exon 20 of 20	ENSP00000563451.1

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

African (AFR) AF: 0.919 AC: 28807 AN: 31352

American (AMR) AF: 0.876 AC: 32917 AN: 37592

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 17561 AN: 23298

East Asian (EAS) AF: 0.668 AC: 26123 AN: 39130

South Asian (SAS) AF: 0.785 AC: 60813 AN: 77482

European-Finnish (FIN) AF: 0.720 AC: 37151 AN: 51566

Middle Eastern (MID) AF: 0.742 AC: 2893 AN: 3898

European-Non Finnish (NFE) AF: 0.760 AC: 825063 AN: 1086224

Other (OTH) AF: 0.772 AC: 44640 AN: 57790

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

African (AFR) AF: 0.917 AC: 38102 AN: 41558

American (AMR) AF: 0.833 AC: 12747 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2614 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3615 AN: 5180

South Asian (SAS) AF: 0.803 AC: 3879 AN: 4828

European-Finnish (FIN) AF: 0.727 AC: 7700 AN: 10596

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51395 AN: 68020

Other (OTH) AF: 0.776 AC: 1639 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.53
PhyloP100		-0.069
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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