rs5746744
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005659.7(UFD1):c.169+125G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 992,450 control chromosomes in the GnomAD database, including 355,097 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.88 ( 58511 hom., cov: 29)
Exomes 𝑓: 0.84 ( 296586 hom. )
Consequence
UFD1
NM_005659.7 intron
NM_005659.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0310
Genes affected
UFD1 (HGNC:12520): (ubiquitin recognition factor in ER associated degradation 1) The protein encoded by this gene forms a complex with two other proteins, nuclear protein localization-4 and valosin-containing protein, and this complex is necessary for the degradation of ubiquitinated proteins. In addition, this complex controls the disassembly of the mitotic spindle and the formation of a closed nuclear envelope after mitosis. Mutations in this gene have been associated with Catch 22 syndrome as well as cardiac and craniofacial defects. Alternative splicing results in multiple transcript variants encoding different isoforms. A related pseudogene has been identified on chromosome 18. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 22-19474943-C-G is Benign according to our data. Variant chr22-19474943-C-G is described in ClinVar as [Benign]. Clinvar id is 1255296.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UFD1 | NM_005659.7 | c.169+125G>C | intron_variant | ENST00000263202.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UFD1 | ENST00000263202.15 | c.169+125G>C | intron_variant | 1 | NM_005659.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.875 AC: 132981AN: 151930Hom.: 58453 Cov.: 29
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GnomAD4 exome AF: 0.839 AC: 705236AN: 840402Hom.: 296586 AF XY: 0.842 AC XY: 362353AN XY: 430466
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GnomAD4 genome ? AF: 0.875 AC: 133100AN: 152048Hom.: 58511 Cov.: 29 AF XY: 0.875 AC XY: 65002AN XY: 74318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at