11-125908410-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_013264.5(DDX25):​c.414C>T​(p.Asn138Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,613,944 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 66 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 60 hom. )

Consequence

DDX25
NM_013264.5 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.337
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 11-125908410-C-T is Benign according to our data. Variant chr11-125908410-C-T is described in ClinVar as [Benign]. Clinvar id is 768496.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.337 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DDX25NM_013264.5 linkc.414C>T p.Asn138Asn synonymous_variant Exon 6 of 12 ENST00000263576.11 NP_037396.3 Q9UHL0-1
DDX25NM_001330438.2 linkc.72C>T p.Asn24Asn synonymous_variant Exon 6 of 12 NP_001317367.1 Q9UHL0-2A0A384NYS3
DDX25XM_047426849.1 linkc.414C>T p.Asn138Asn synonymous_variant Exon 6 of 11 XP_047282805.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DDX25ENST00000263576.11 linkc.414C>T p.Asn138Asn synonymous_variant Exon 6 of 12 1 NM_013264.5 ENSP00000263576.6 Q9UHL0-1

Frequencies

GnomAD3 genomes
AF:
0.0149
AC:
2261
AN:
152134
Hom.:
67
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0519
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.0115
GnomAD3 exomes
AF:
0.00390
AC:
972
AN:
249244
Hom.:
31
AF XY:
0.00306
AC XY:
414
AN XY:
135210
show subpopulations
Gnomad AFR exome
AF:
0.0564
Gnomad AMR exome
AF:
0.00185
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000556
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000221
Gnomad OTH exome
AF:
0.000826
GnomAD4 exome
AF:
0.00154
AC:
2253
AN:
1461692
Hom.:
60
Cov.:
33
AF XY:
0.00128
AC XY:
932
AN XY:
727124
show subpopulations
Gnomad4 AFR exome
AF:
0.0543
Gnomad4 AMR exome
AF:
0.00239
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000110
Gnomad4 OTH exome
AF:
0.00305
GnomAD4 genome
AF:
0.0149
AC:
2269
AN:
152252
Hom.:
66
Cov.:
32
AF XY:
0.0144
AC XY:
1073
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.0519
Gnomad4 AMR
AF:
0.00451
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.0113
Alfa
AF:
0.00504
Hom.:
13
Bravo
AF:
0.0170
Asia WGS
AF:
0.00404
AC:
15
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000356

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Apr 19, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
9.0
DANN
Benign
0.74

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: rs34007659; hg19: chr11-125778305; API