11-108839045-T-A

Position:

• chr11-108839045-T-A

Variant summary

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

The NM_004398.4(DDX10):​c.2085+480T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,070 control chromosomes in the GnomAD database, including 22,453 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 0.53 (22453 hom., cov: 32)
• Consequence: DDX10 NM_004398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741

Genes affected

DDX10 (HGNC:2735): (DEAD-box helicase 10) 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 family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, and it may be involved in ribosome assembly. Fusion of this gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX10	NM_004398.4	c.2085+480T>A		intron_variant		ENST00000322536.8	NP_004389.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX10	ENST00000322536.8	c.2085+480T>A		intron_variant		1	NM_004398.4	ENSP00000314348	P2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80461 AN: 151952 Hom.: 22437 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.529 AC: 80520 AN: 152070 Hom.: 22453 Cov.: 32 AF XY: 0.528 AC XY: 39208 AN XY: 74326

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.543

Alfa AF: 0.575 Hom.: 3232

Bravo AF: 0.524

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.54

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: rs10890898; hg19: chr11-108709772;