11-125908055-G-T

Position:

• chr11-125908055-G-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.312-141G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00894 in 658,320 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.025 (120 hom., cov: 33)
  • Exomes 𝑓: 0.0042 (73 hom.)
• Consequence: DDX25 NM_013264.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.34

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 11-125908055-G-T is Benign according to our data. Variant chr11-125908055-G-T is described in ClinVar as [Benign]. Clinvar id is 1277621.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX25	NM_013264.5	c.312-141G>T		intron_variant		ENST00000263576.11	NP_037396.3
DDX25	NM_001330438.2	c.-31-141G>T		intron_variant			NP_001317367.1
DDX25	XM_047426849.1	c.312-141G>T		intron_variant			XP_047282805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX25	ENST00000263576.11	c.312-141G>T		intron_variant		1	NM_013264.5	ENSP00000263576.6

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3731 AN: 152136 Hom.: 120 Cov.: 33

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00988

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.0216

GnomAD4 exome AF: 0.00424 AC: 2145 AN: 506066 Hom.: 73 AF XY: 0.00406 AC XY: 1081 AN XY: 266192

Gnomad4 AFR exome AF: 0.0881

Gnomad4 AMR exome AF: 0.00524

Gnomad4 ASJ exome AF: 0.00792

Gnomad4 EAS exome AF: 0.0000637

Gnomad4 SAS exome AF: 0.00907

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000292

Gnomad4 OTH exome AF: 0.00826

GnomAD4 genome AF: 0.0246 AC: 3743 AN: 152254 Hom.: 120 Cov.: 33 AF XY: 0.0242 AC XY: 1799 AN XY: 74450

Gnomad4 AFR AF: 0.0829

Gnomad4 AMR AF: 0.00987

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000382

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.0125 Hom.: 14

Bravo AF: 0.0276

Asia WGS AF: 0.00895 AC: 31 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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.62

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: rs76286501; hg19: chr11-125777950;