11-118752276-T-C

Position:

• chr11-118752276-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004397.6(DDX6):​c.*8-179A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,068 control chromosomes in the GnomAD database, including 3,959 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (3959 hom., cov: 31)
• Consequence: DDX6 NM_004397.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.26

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 11-118752276-T-C is Benign according to our data. Variant chr11-118752276-T-C is described in ClinVar as [Benign]. Clinvar id is 1300447.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX6	NM_004397.6	c.*8-179A>G		intron_variant		ENST00000534980.7	NP_004388.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX6	ENST00000534980.7	c.*8-179A>G		intron_variant		1	NM_004397.6	ENSP00000442266.1
DDX6	ENST00000620157.4	c.*8-179A>G		intron_variant		1		ENSP00000478754.1
DDX6	ENST00000529162.1	n.1063-179A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34143 AN: 151946 Hom.: 3957 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.225 AC: 34154 AN: 152068 Hom.: 3959 Cov.: 31 AF XY: 0.225 AC XY: 16701 AN XY: 74340

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.246

Alfa AF: 0.227 Hom.: 719

Bravo AF: 0.216

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-1.0
CADD	Benign	0.19
DANN	Benign	0.19

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: rs3825057; hg19: chr11-118622985;