7-107563971-G-GGGCCC
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_181581.3(DUS4L):c.-349_-348insGGCCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000099 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DUS4L
NM_181581.3 5_prime_UTR
NM_181581.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.556
Genes affected
DUS4L (HGNC:21517): (dihydrouridine synthase 4 like) Predicted to enable tRNA dihydrouridine synthase activity. Predicted to be involved in tRNA dihydrouridine synthesis. [provided by Alliance of Genome Resources, Apr 2022]
COG5 (HGNC:14857): (component of oligomeric golgi complex 5) The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. The encoded protein is organized with conserved oligomeric Golgi complex components 6, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants. Mutations in this gene result in congenital disorder of glycosylation type 2I.[provided by RefSeq, Jan 2011]
DUS4L-BCAP29 (HGNC:54422): (DUS4L-BCAP29 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring DUS4L (dihydrouridine synthase 4 like) and BCAP29 (B cell receptor associated protein 29) genes on chromosome 7. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2019]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-107563971-G-GGGCCC is Pathogenic according to our data. Variant chr7-107563971-G-GGGCCC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 638408.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DUS4L | ENST00000265720 | c.-349_-348insGGCCC | 5_prime_UTR_variant | Exon 1 of 8 | 2 | NM_181581.3 | ENSP00000265720.3 | |||
| DUS4L-BCAP29 | ENST00000673757 | c.-349_-348insGGCCC | 5_prime_UTR_variant | Exon 1 of 15 | ENSP00000501026.1 | |||||
| COG5 | ENST00000297135.9 | c.-76_-75insGGGCC | upstream_gene_variant | 1 | NM_006348.5 | ENSP00000297135.4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000991 AC: 139AN: 1402084Hom.: 0 Cov.: 24 AF XY: 0.0000776 AC XY: 54AN XY: 696086
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
139
AN:
1402084
Hom.:
Cov.:
24
AF XY:
AC XY:
54
AN XY:
696086
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
COG5-congenital disorder of glycosylation Pathogenic:1
Apr 27, 2019
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at