11-125908324-T-C

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.246
Variant links:
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]

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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
DDX25NM_013264.5 linkuse as main transcriptc.404+36T>C intron_variant ENST00000263576.11 NP_037396.3 Q9UHL0-1
DDX25NM_001330438.2 linkuse as main transcriptc.62+36T>C intron_variant NP_001317367.1 Q9UHL0-2A0A384NYS3
DDX25XM_047426849.1 linkuse as main transcriptc.404+36T>C intron_variant XP_047282805.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DDX25ENST00000263576.11 linkuse as main transcriptc.404+36T>C intron_variant 1 NM_013264.5 ENSP00000263576.6 Q9UHL0-1

Frequencies

GnomAD3 genomes
AF:
0.0203
AC:
3090
AN:
152172
Hom.:
96
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0672
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00818
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.0190
Gnomad SAS
AF:
0.00373
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000514
Gnomad OTH
AF:
0.0119
GnomAD3 exomes
AF:
0.00741
AC:
1841
AN:
248582
Hom.:
47
AF XY:
0.00604
AC XY:
814
AN XY:
134872
show subpopulations
Gnomad AFR exome
AF:
0.0709
Gnomad AMR exome
AF:
0.00465
Gnomad ASJ exome
AF:
0.00149
Gnomad EAS exome
AF:
0.0228
Gnomad SAS exome
AF:
0.00220
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000550
Gnomad OTH exome
AF:
0.00514
GnomAD4 exome
AF:
0.00304
AC:
4444
AN:
1460592
Hom.:
119
Cov.:
32
AF XY:
0.00269
AC XY:
1958
AN XY:
726602
show subpopulations
Gnomad4 AFR exome
AF:
0.0724
Gnomad4 AMR exome
AF:
0.00545
Gnomad4 ASJ exome
AF:
0.00138
Gnomad4 EAS exome
AF:
0.0186
Gnomad4 SAS exome
AF:
0.00229
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000332
Gnomad4 OTH exome
AF:
0.00625
GnomAD4 genome
AF:
0.0203
AC:
3094
AN:
152290
Hom.:
95
Cov.:
32
AF XY:
0.0197
AC XY:
1467
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0671
Gnomad4 AMR
AF:
0.00817
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.0193
Gnomad4 SAS
AF:
0.00332
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000515
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.0132
Hom.:
8
Bravo
AF:
0.0236
Asia WGS
AF:
0.0210
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.4
DANN
Benign
0.52

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12285354; hg19: chr11-125778219; COSMIC: COSV54988686; API