11-5516102-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145053.5(UBQLNL):c.340C>T(p.Arg114Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145053.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBQLNL | NM_145053.5 | c.340C>T | p.Arg114Trp | missense_variant | 1/1 | ENST00000380184.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLNL | ENST00000380184.2 | c.340C>T | p.Arg114Trp | missense_variant | 1/1 | NM_145053.5 | A2 | ||
UBQLNL | ENST00000673910.1 | c.310C>T | p.Arg104Trp | missense_variant | 2/2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250778Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135480
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461764Hom.: 0 Cov.: 35 AF XY: 0.000133 AC XY: 97AN XY: 727168
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.340C>T (p.R114W) alteration is located in exon 1 (coding exon 1) of the UBQLNL gene. This alteration results from a C to T substitution at nucleotide position 340, causing the arginine (R) at amino acid position 114 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at