11-5515095-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145053.5(UBQLNL):c.1347G>A(p.Met449Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,106 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
Genome browser will be placed here
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.1347G>A | p.Met449Ile | missense_variant | 1/1 | ENST00000380184.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLNL | ENST00000380184.2 | c.1347G>A | p.Met449Ile | missense_variant | 1/1 | NM_145053.5 | A2 | ||
UBQLNL | ENST00000673910.1 | c.1317G>A | p.Met439Ile | missense_variant | 2/2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250932Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135584
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461868Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727234
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.1347G>A (p.M449I) alteration is located in exon 1 (coding exon 1) of the UBQLNL gene. This alteration results from a G to A substitution at nucleotide position 1347, causing the methionine (M) at amino acid position 449 to be replaced by an isoleucine (I). 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