chr22-19478942-C-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005659.7(UFD1):c.3+141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,169,476 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 21 hom., cov: 33)
Exomes 𝑓: 0.012 ( 128 hom. )
Consequence
UFD1
NM_005659.7 intron
NM_005659.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.379
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 22-19478942-C-G is Benign according to our data. Variant chr22-19478942-C-G is described in ClinVar as [Benign]. Clinvar id is 1261224.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 21 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UFD1 | NM_005659.7 | c.3+141G>C | intron_variant | ENST00000263202.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UFD1 | ENST00000263202.15 | c.3+141G>C | intron_variant | 1 | NM_005659.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0109 AC: 1659AN: 152188Hom.: 21 Cov.: 33
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GnomAD4 exome AF: 0.0116 AC: 11825AN: 1017172Hom.: 128 Cov.: 13 AF XY: 0.0117 AC XY: 5952AN XY: 507886
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GnomAD4 genome AF: 0.0109 AC: 1656AN: 152304Hom.: 21 Cov.: 33 AF XY: 0.0127 AC XY: 946AN XY: 74480
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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 25, 2021 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at