12-113169697-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024072.4(DDX54):​c.1414+73A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,546,162 control chromosomes in the GnomAD database, including 26,679 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3564 hom., cov: 32)
Exomes 𝑓: 0.18 ( 23115 hom. )

Consequence

DDX54
NM_024072.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.86
Variant links:
Genes affected
DDX54 (HGNC:20084): (DEAD-box helicase 54) This gene encodes a member of the DEAD box protein family. 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 this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The nucleolar protein encoded by this gene interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. Alternative splice variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DDX54NM_024072.4 linkuse as main transcriptc.1414+73A>G intron_variant ENST00000306014.10
DDX54NM_001111322.2 linkuse as main transcriptc.1414+73A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DDX54ENST00000306014.10 linkuse as main transcriptc.1414+73A>G intron_variant 1 NM_024072.4 A1Q8TDD1-1
DDX54ENST00000314045.11 linkuse as main transcriptc.1414+73A>G intron_variant 1 P3Q8TDD1-2

Frequencies

GnomAD3 genomes
AF:
0.210
AC:
31905
AN:
152002
Hom.:
3540
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.294
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.161
Gnomad ASJ
AF:
0.213
Gnomad EAS
AF:
0.235
Gnomad SAS
AF:
0.171
Gnomad FIN
AF:
0.228
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.169
Gnomad OTH
AF:
0.190
GnomAD4 exome
AF:
0.178
AC:
248790
AN:
1394042
Hom.:
23115
AF XY:
0.178
AC XY:
122897
AN XY:
689018
show subpopulations
Gnomad4 AFR exome
AF:
0.284
Gnomad4 AMR exome
AF:
0.132
Gnomad4 ASJ exome
AF:
0.207
Gnomad4 EAS exome
AF:
0.258
Gnomad4 SAS exome
AF:
0.170
Gnomad4 FIN exome
AF:
0.221
Gnomad4 NFE exome
AF:
0.171
Gnomad4 OTH exome
AF:
0.191
GnomAD4 genome
AF:
0.210
AC:
31970
AN:
152120
Hom.:
3564
Cov.:
32
AF XY:
0.212
AC XY:
15754
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.294
Gnomad4 AMR
AF:
0.161
Gnomad4 ASJ
AF:
0.213
Gnomad4 EAS
AF:
0.234
Gnomad4 SAS
AF:
0.171
Gnomad4 FIN
AF:
0.228
Gnomad4 NFE
AF:
0.169
Gnomad4 OTH
AF:
0.196
Alfa
AF:
0.178
Hom.:
382
Bravo
AF:
0.209
Asia WGS
AF:
0.229
AC:
796
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.11
DANN
Benign
0.79
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs2384207; hg19: chr12-113607502; API