chr1-156041545-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_020131.5(UBQLN4):c.1593C>T(p.Ser531=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00785 in 1,612,624 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0059 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0081 ( 59 hom. )
Consequence
UBQLN4
NM_020131.5 synonymous
NM_020131.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.129
Genes affected
UBQLN4 (HGNC:1237): (ubiquilin 4) Enables K48-linked polyubiquitin modification-dependent protein binding activity and identical protein binding activity. Involved in cellular response to DNA damage stimulus; negative regulation of double-strand break repair via homologous recombination; and regulation of cellular catabolic process. Located in several cellular components, including autophagosome; nucleoplasm; and site of DNA damage. Part of protein-containing complex. Colocalizes with cytosolic proteasome complex and nuclear proteasome complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 1-156041545-G-A is Benign according to our data. Variant chr1-156041545-G-A is described in ClinVar as [Benign]. Clinvar id is 781585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.129 with no splicing effect.
BS2
High AC in GnomAd4 at 898 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBQLN4 | NM_020131.5 | c.1593C>T | p.Ser531= | synonymous_variant | 10/11 | ENST00000368309.4 | NP_064516.2 | |
UBQLN4 | NM_001304342.2 | c.1533C>T | p.Ser511= | synonymous_variant | 10/11 | NP_001291271.1 | ||
UBQLN4 | XM_024448469.2 | c.1593C>T | p.Ser531= | synonymous_variant | 10/11 | XP_024304237.1 | ||
UBQLN4 | XM_047425666.1 | c.1059C>T | p.Ser353= | synonymous_variant | 10/11 | XP_047281622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBQLN4 | ENST00000368309.4 | c.1593C>T | p.Ser531= | synonymous_variant | 10/11 | 1 | NM_020131.5 | ENSP00000357292 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00590 AC: 898AN: 152208Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00631 AC: 1580AN: 250384Hom.: 10 AF XY: 0.00641 AC XY: 867AN XY: 135316
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GnomAD4 exome AF: 0.00806 AC: 11763AN: 1460298Hom.: 59 Cov.: 30 AF XY: 0.00783 AC XY: 5686AN XY: 726488
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GnomAD4 genome AF: 0.00590 AC: 898AN: 152326Hom.: 2 Cov.: 32 AF XY: 0.00556 AC XY: 414AN XY: 74478
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Aug 28, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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