13-30621148-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005800.5(USPL1):c.8A>T(p.Asp3Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000187 in 1,605,364 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.8A>T | p.Asp3Val | missense_variant | Exon 2 of 9 | 1 | NM_005800.5 | ENSP00000255304.4 | ||
USPL1 | ENST00000614860.1 | c.-248-616A>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000480656.1 | ||||
USPL1 | ENST00000465952.5 | n.365-616A>T | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243766Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132014
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1453264Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 722436
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.8A>T (p.D3V) alteration is located in exon 2 (coding exon 1) of the USPL1 gene. This alteration results from a A to T substitution at nucleotide position 8, causing the aspartic acid (D) at amino acid position 3 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