X-56564452-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_013444.4(UBQLN2):c.579C>T(p.Ser193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,209,561 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000036 ( 0 hom. 12 hem. )
Consequence
UBQLN2
NM_013444.4 synonymous
NM_013444.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.23
Genes affected
UBQLN2 (HGNC:12509): (ubiquilin 2) This gene encodes an ubiquitin-like protein (ubiquilin) that shares high degree of similarity with related products in yeast, rat and frog. Ubiquilins contain a N-terminal ubiquitin-like domain and a C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases; and thus, are thought to functionally link the ubiquitination machinery to the proteasome to affect in vivo protein degradation. This ubiquilin has also been shown to bind the ATPase domain of the Hsp70-like Stch protein. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant X-56564452-C-T is Benign according to our data. Variant chrX-56564452-C-T is described in ClinVar as [Benign]. Clinvar id is 586918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.23 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000538 (6/111587) while in subpopulation AMR AF= 0.000473 (5/10580). AF 95% confidence interval is 0.000186. There are 0 homozygotes in gnomad4. There are 0 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Hemizygotes in GnomAdExome4 at 12 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBQLN2 | NM_013444.4 | c.579C>T | p.Ser193= | synonymous_variant | 1/1 | ENST00000338222.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLN2 | ENST00000338222.7 | c.579C>T | p.Ser193= | synonymous_variant | 1/1 | NM_013444.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000538 AC: 6AN: 111587Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33767
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GnomAD3 exomes AF: 0.000186 AC: 34AN: 183077Hom.: 0 AF XY: 0.000148 AC XY: 10AN XY: 67573
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GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097974Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 12AN XY: 363336
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GnomAD4 genome AF: 0.0000538 AC: 6AN: 111587Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33767
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 28, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 17, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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