11-118752035-G-A

Position:

• chr11-118752035-G-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_004397.6(DDX6):​c.*70C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.989 in 282,990 control chromosomes in the GnomAD database, including 138,503 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.99 (74623 hom., cov: 32)
  • Exomes 𝑓: 0.99 (63880 hom.)
• Consequence: DDX6 NM_004397.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 4.14

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]

DDX6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP6: Variant 11-118752035-G-A is Benign according to our data. Variant chr11-118752035-G-A is described in ClinVar as [Benign]. Clinvar id is 1300455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX6	NM_004397.6	c.*70C>T		3_prime_UTR_variant	14/14	ENST00000534980.7	NP_004388.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX6	ENST00000534980	c.*70C>T		3_prime_UTR_variant	14/14	1	NM_004397.6	ENSP00000442266.1
DDX6	ENST00000620157	c.*70C>T		3_prime_UTR_variant	14/14	1		ENSP00000478754.1
DDX6	ENST00000529162.1	n.1125C>T		non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150637 AN: 152186 Hom.: 74562 Cov.: 32

Gnomad AFR AF: 0.997

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.991

GnomAD4 exome AF: 0.989 AC: 129208 AN: 130686 Hom.: 63880 Cov.: 0 AF XY: 0.989 AC XY: 73623 AN XY: 74428

Gnomad4 AFR exome AF: 0.997

Gnomad4 AMR exome AF: 0.994

Gnomad4 ASJ exome AF: 0.997

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.993

Gnomad4 FIN exome AF: 0.983

Gnomad4 NFE exome AF: 0.986

Gnomad4 OTH exome AF: 0.989

GnomAD4 genome AF: 0.990 AC: 150757 AN: 152304 Hom.: 74623 Cov.: 32 AF XY: 0.989 AC XY: 73695 AN XY: 74478

Gnomad4 AFR AF: 0.997

Gnomad4 AMR AF: 0.993

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.976

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.991

Alfa AF: 0.987 Hom.: 42865

Bravo AF: 0.991

Asia WGS AF: 0.996 AC: 3464 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	15
DANN	Benign	0.93

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: rs6589689; hg19: chr11-118622744;