chr11-125904062-G-C

Position:

• chr11-125904062-G-C

Variant summary

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

The NM_001330438.2(DDX25):​c.-280+632G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,212 control chromosomes in the GnomAD database, including 50,714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.81 (50714 hom., cov: 34)
• Consequence: DDX25 NM_001330438.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0150

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=-0.89).
• BP6: Variant 11-125904062-G-C is Benign according to our data. Variant chr11-125904062-G-C is described in ClinVar as [Benign]. Clinvar id is 1266919.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX25	NM_001330438.2	c.-280+632G>C		intron_variant			NP_001317367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX25	ENST00000525943.1	c.-280+632G>C		intron_variant		5		ENSP00000490224.1
ENSG00000255027	ENST00000533033.2	n.395-693C>G		intron_variant		4
DDX25	ENST00000637851.1	n.-213+632G>C		intron_variant		5		ENSP00000490392.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123215 AN: 152094 Hom.: 50673 Cov.: 34

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.810 AC: 123315 AN: 152212 Hom.: 50714 Cov.: 34 AF XY: 0.812 AC XY: 60422 AN XY: 74422

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.809

Alfa AF: 0.838 Hom.: 6309

Bravo AF: 0.805

Asia WGS AF: 0.862 AC: 2997 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 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1554526; hg19: chr11-125773957;