chr13-30621237-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005800.5(USPL1):c.97A>G(p.Lys33Glu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000035 in 1,429,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005800.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USPL1 | NM_005800.5 | c.97A>G | p.Lys33Glu | missense_variant, splice_region_variant | 2/9 | ENST00000255304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.97A>G | p.Lys33Glu | missense_variant, splice_region_variant | 2/9 | 1 | NM_005800.5 | P1 | |
USPL1 | ENST00000614860.1 | c.-248-527A>G | intron_variant | 1 | |||||
USPL1 | ENST00000465952.5 | n.365-527A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000919 AC: 2AN: 217556Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118052
GnomAD4 exome AF: 0.00000350 AC: 5AN: 1429294Hom.: 0 Cov.: 30 AF XY: 0.00000705 AC XY: 5AN XY: 709568
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.97A>G (p.K33E) alteration is located in exon 2 (coding exon 1) of the USPL1 gene. This alteration results from a A to G substitution at nucleotide position 97, causing the lysine (K) at amino acid position 33 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