11-125908324-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013264.5(DDX25):c.404+36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 1,612,882 control chromosomes in the GnomAD database, including 214 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 95 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 119 hom. )
Consequence
DDX25
NM_013264.5 intron
NM_013264.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.246
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 11-125908324-T-C is Benign according to our data. Variant chr11-125908324-T-C is described in ClinVar as [Benign]. Clinvar id is 1251045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.065 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX25 | NM_013264.5 | c.404+36T>C | intron_variant | ENST00000263576.11 | NP_037396.3 | |||
DDX25 | NM_001330438.2 | c.62+36T>C | intron_variant | NP_001317367.1 | ||||
DDX25 | XM_047426849.1 | c.404+36T>C | intron_variant | XP_047282805.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX25 | ENST00000263576.11 | c.404+36T>C | intron_variant | 1 | NM_013264.5 | ENSP00000263576.6 |
Frequencies
GnomAD3 genomes AF: 0.0203 AC: 3090AN: 152172Hom.: 96 Cov.: 32
GnomAD3 genomes
AF:
AC:
3090
AN:
152172
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00741 AC: 1841AN: 248582Hom.: 47 AF XY: 0.00604 AC XY: 814AN XY: 134872
GnomAD3 exomes
AF:
AC:
1841
AN:
248582
Hom.:
AF XY:
AC XY:
814
AN XY:
134872
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00304 AC: 4444AN: 1460592Hom.: 119 Cov.: 32 AF XY: 0.00269 AC XY: 1958AN XY: 726602
GnomAD4 exome
AF:
AC:
4444
AN:
1460592
Hom.:
Cov.:
32
AF XY:
AC XY:
1958
AN XY:
726602
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0203 AC: 3094AN: 152290Hom.: 95 Cov.: 32 AF XY: 0.0197 AC XY: 1467AN XY: 74474
GnomAD4 genome
AF:
AC:
3094
AN:
152290
Hom.:
Cov.:
32
AF XY:
AC XY:
1467
AN XY:
74474
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
73
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at