chr11-5515529-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_145053.5(UBQLNL):c.913C>T(p.Gln305Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,108 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0079 ( 12 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 20 hom. )
Consequence
UBQLNL
NM_145053.5 stop_gained
NM_145053.5 stop_gained
Scores
1
6
Clinical Significance
Conservation
PhyloP100: 0.254
Genes affected
UBQLNL (HGNC:28294): (ubiquilin like) Predicted to enable polyubiquitin modification-dependent protein binding activity. Predicted to be involved in ubiquitin-dependent protein catabolic process. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM4
?
Stoplost variant in NM_145053.5 Downstream stopcodon found after 561 codons.
BP6
?
Variant 11-5515529-G-A is Benign according to our data. Variant chr11-5515529-G-A is described in ClinVar as [Benign]. Clinvar id is 715487.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00795 (1210/152272) while in subpopulation AFR AF= 0.0238 (991/41556). AF 95% confidence interval is 0.0226. There are 12 homozygotes in gnomad4. There are 578 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBQLNL | NM_145053.5 | c.913C>T | p.Gln305Ter | stop_gained | 1/1 | ENST00000380184.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLNL | ENST00000380184.2 | c.913C>T | p.Gln305Ter | stop_gained | 1/1 | NM_145053.5 | A2 | ||
UBQLNL | ENST00000673910.1 | c.883C>T | p.Gln295Ter | stop_gained | 2/2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00791 AC: 1203AN: 152154Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00317 AC: 796AN: 251054Hom.: 5 AF XY: 0.00256 AC XY: 347AN XY: 135652
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GnomAD4 exome AF: 0.00162 AC: 2364AN: 1461836Hom.: 20 Cov.: 92 AF XY: 0.00155 AC XY: 1125AN XY: 727210
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GnomAD4 genome ? AF: 0.00795 AC: 1210AN: 152272Hom.: 12 Cov.: 32 AF XY: 0.00776 AC XY: 578AN XY: 74452
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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 | Invitae | Sep 21, 2017 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
N;D
Vest4
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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