13-30621849-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005800.5(USPL1):c.185G>A(p.Arg62Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000525 in 1,580,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.185G>A | p.Arg62Gln | missense_variant | Exon 3 of 9 | 1 | NM_005800.5 | ENSP00000255304.4 | ||
USPL1 | ENST00000614860 | c.-163G>A | 5_prime_UTR_variant | Exon 2 of 7 | 1 | ENSP00000480656.1 | ||||
USPL1 | ENST00000465952.5 | n.450G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000118 AC: 27AN: 229250Hom.: 0 AF XY: 0.0000800 AC XY: 10AN XY: 124936
GnomAD4 exome AF: 0.0000553 AC: 79AN: 1428926Hom.: 0 Cov.: 30 AF XY: 0.0000549 AC XY: 39AN XY: 710670
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.185G>A (p.R62Q) alteration is located in exon 3 (coding exon 2) of the USPL1 gene. This alteration results from a G to A substitution at nucleotide position 185, causing the arginine (R) at amino acid position 62 to be replaced by a glutamine (Q). 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