13-30630997-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001321532.2(USPL1):c.-153A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001321532.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.391A>G | p.Ile131Val | missense_variant | Exon 4 of 9 | 1 | NM_005800.5 | ENSP00000255304.4 | ||
USPL1 | ENST00000614860.1 | c.-119-6747A>G | intron_variant | Intron 2 of 6 | 1 | ENSP00000480656.1 | ||||
USPL1 | ENST00000465952.5 | n.656A>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250938Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135646
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727192
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.391A>G (p.I131V) alteration is located in exon 4 (coding exon 3) of the USPL1 gene. This alteration results from a A to G substitution at nucleotide position 391, causing the isoleucine (I) at amino acid position 131 to be replaced by a valine (V). 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