chr11-125904265-TCGCCCCGCTCTCTGCCCTC-T

Position:

• chr11-125904265-TCGCCCCGCTCTCTGCCCTC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001330438.2(DDX25):​c.-280+872_-280+890delTCCGCCCCGCTCTCTGCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 338,436 control chromosomes in the GnomAD database, including 67,975 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.62 (29117 hom., cov: 0)
  • Exomes 𝑓: 0.63 (38858 hom.)
• Consequence: DDX25 NM_001330438.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.661

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 -10 ACMG points.

• BP6: Variant 11-125904265-TCGCCCCGCTCTCTGCCCTC-T is Benign according to our data. Variant chr11-125904265-TCGCCCCGCTCTCTGCCCTC-T is described in ClinVar as [Benign]. Clinvar id is 1250886.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX25	NM_001330438.2	c.-280+872_-280+890delTCCGCCCCGCTCTCTGCCC		intron_variant			NP_001317367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX25	ENST00000525943.1	c.-280+872_-280+890delTCCGCCCCGCTCTCTGCCC		intron_variant		5		ENSP00000490224.1
ENSG00000255027	ENST00000533033.2	n.395-915_395-897delGAGGGCAGAGAGCGGGGCG		intron_variant		4
DDX25	ENST00000637851.1	n.-213+872_-213+890delTCCGCCCCGCTCTCTGCCC		intron_variant		5		ENSP00000490392.1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 92696 AN: 149036 Hom.: 29091 Cov.: 0

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.614

GnomAD4 exome AF: 0.634 AC: 120033 AN: 189294 Hom.: 38858 AF XY: 0.635 AC XY: 61468 AN XY: 96864

Gnomad4 AFR exome AF: 0.551

Gnomad4 AMR exome AF: 0.691

Gnomad4 ASJ exome AF: 0.658

Gnomad4 EAS exome AF: 0.722

Gnomad4 SAS exome AF: 0.714

Gnomad4 FIN exome AF: 0.613

Gnomad4 NFE exome AF: 0.624

Gnomad4 OTH exome AF: 0.624

GnomAD4 genome AF: 0.622 AC: 92771 AN: 149142 Hom.: 29117 Cov.: 0 AF XY: 0.623 AC XY: 45357 AN XY: 72746

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.616

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

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201190482; hg19: chr11-125774160;