11-125906472-C-T

Position:

• chr11-125906472-C-T

Variant summary

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

The NM_013264.5(DDX25):​c.311+263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,706 control chromosomes in the GnomAD database, including 3,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3281 hom., cov: 28)
• Consequence: DDX25 NM_013264.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.19

Genes affected

DDX25 (HGNC:18698): (DEAD-box helicase 25) 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 the 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 encoded protein is a gonadotropin-regulated and developmentally expressed testicular RNA helicase. It may serve to maintain testicular functions related to steroidogenesis and spermatogenesis. [provided by RefSeq, Jul 2008]

ENSG00000255027 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 11-125906472-C-T is Benign according to our data. Variant chr11-125906472-C-T is described in ClinVar as [Benign]. Clinvar id is 1258301.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX25	NM_013264.5	c.311+263C>T		intron_variant		ENST00000263576.11	NP_037396.3
DDX25	NM_001330438.2	c.-32+263C>T		intron_variant			NP_001317367.1
DDX25	XM_047426849.1	c.311+263C>T		intron_variant			XP_047282805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX25	ENST00000263576.11	c.311+263C>T		intron_variant		1	NM_013264.5	ENSP00000263576.6

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29199 AN: 151588 Hom.: 3282 Cov.: 28

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.193 AC: 29204 AN: 151706 Hom.: 3281 Cov.: 28 AF XY: 0.191 AC XY: 14172 AN XY: 74126

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.199

Alfa AF: 0.116 Hom.: 214

Bravo AF: 0.187

Asia WGS AF: 0.159 AC: 556 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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.57

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: rs78086532; hg19: chr11-125776367;