chr13-30631034-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005800.5(USPL1):c.428G>A(p.Gly143Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.428G>A | p.Gly143Glu | missense_variant | 4/9 | ENST00000255304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.428G>A | p.Gly143Glu | missense_variant | 4/9 | 1 | NM_005800.5 | P1 | |
USPL1 | ENST00000614860.1 | c.-119-6710G>A | intron_variant | 1 | |||||
USPL1 | ENST00000465952.5 | n.693G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000438 AC: 110AN: 250858Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135604
GnomAD4 exome AF: 0.000273 AC: 399AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.000253 AC XY: 184AN XY: 727210
GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.428G>A (p.G143E) alteration is located in exon 4 (coding exon 3) of the USPL1 gene. This alteration results from a G to A substitution at nucleotide position 428, causing the glycine (G) at amino acid position 143 to be replaced by a glutamic acid (E). 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