7-107563995-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_181581.3(DUS4L):c.-325C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,561,280 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_181581.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DUS4L | ENST00000265720 | c.-325C>T | 5_prime_UTR_variant | Exon 1 of 8 | 2 | NM_181581.3 | ENSP00000265720.3 | |||
DUS4L-BCAP29 | ENST00000673757 | c.-325C>T | 5_prime_UTR_variant | Exon 1 of 15 | ENSP00000501026.1 | |||||
COG5 | ENST00000297135.9 | c.-99G>A | upstream_gene_variant | 1 | NM_006348.5 | ENSP00000297135.4 |
Frequencies
GnomAD3 genomes AF: 0.0137 AC: 2077AN: 152150Hom.: 55 Cov.: 32
GnomAD3 exomes AF: 0.00302 AC: 477AN: 158134Hom.: 7 AF XY: 0.00257 AC XY: 223AN XY: 86614
GnomAD4 exome AF: 0.00148 AC: 2083AN: 1409012Hom.: 40 Cov.: 38 AF XY: 0.00127 AC XY: 885AN XY: 696618
GnomAD4 genome AF: 0.0137 AC: 2083AN: 152268Hom.: 55 Cov.: 32 AF XY: 0.0128 AC XY: 953AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
COG5-congenital disorder of glycosylation Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
COG5-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at