rs2077579

chr11-118748338-T-G

Variant summary

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

The NM_004397.6(DDX6):c.*3767A>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 0.171 in 151,896 control chromosomes in the GnomAD database, including 2,486 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 0.17 (2486 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: DDX6 NM_004397.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

Genes affected

DDX6 (HGNC:2747): (DEAD-box helicase 6) This gene encodes a member of the DEAD box protein family. The protein is an RNA helicase found in P-bodies and stress granules, and functions in translation suppression and mRNA degradation. It is required for microRNA-induced gene silencing. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Mar 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDX6	NM_004397.6	c.*3767A>C		3_prime_UTR_variant	14/14	ENST00000534980.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX6	ENST00000534980.7	c.*3767A>C		3_prime_UTR_variant	14/14	1	NM_004397.6	P1
DDX6	ENST00000620157.4	c.*3767A>C		3_prime_UTR_variant	14/14	1		P1
	ENST00000526274.2	n.374-1875T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26045 AN: 151778 Hom.: 2482 Cov.: 31

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.165

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.171 AC: 26049 AN: 151896 Hom.: 2486 Cov.: 31 AF XY: 0.174 AC XY: 12917 AN XY: 74230

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.164

Alfa AF: 0.200 Hom.: 4322

Bravo AF: 0.159

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	18
Dann	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2077579; hg19: chr11-118619047;