chr13-30631399-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005800.5(USPL1):c.793A>C(p.Ile265Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,614,260 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I265V) has been classified as Likely benign.
Frequency
Consequence
NM_005800.5 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 |
---|---|---|---|---|---|---|---|
USPL1 | NM_005800.5 | c.793A>C | p.Ile265Leu | missense_variant | 4/9 | ENST00000255304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.793A>C | p.Ile265Leu | missense_variant | 4/9 | 1 | NM_005800.5 | P1 | |
USPL1 | ENST00000614860.1 | c.-119-6345A>C | intron_variant | 1 | |||||
USPL1 | ENST00000465952.5 | n.1058A>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000406 AC: 102AN: 251372Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135852
GnomAD4 exome AF: 0.000289 AC: 423AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.000296 AC XY: 215AN XY: 727244
GnomAD4 genome ? AF: 0.000400 AC: 61AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.000429 AC XY: 32AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.793A>C (p.I265L) alteration is located in exon 4 (coding exon 3) of the USPL1 gene. This alteration results from a A to C substitution at nucleotide position 793, causing the isoleucine (I) at amino acid position 265 to be replaced by a leucine (L). 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