4-143185968-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032557.6(USP38):c.518G>A(p.Arg173Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,614,182 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032557.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP38 | NM_032557.6 | c.518G>A | p.Arg173Gln | missense_variant | Exon 1 of 10 | ENST00000307017.9 | NP_115946.2 | |
USP38 | NM_001410848.1 | c.518G>A | p.Arg173Gln | missense_variant | Exon 1 of 9 | NP_001397777.1 | ||
USP38 | NM_001290325.1 | c.518G>A | p.Arg173Gln | missense_variant | Exon 1 of 9 | NP_001277254.1 | ||
USP38 | NM_001290326.1 | c.-964G>A | 5_prime_UTR_variant | Exon 1 of 11 | NP_001277255.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251468Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135906
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 727240
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.518G>A (p.R173Q) alteration is located in exon 1 (coding exon 1) of the USP38 gene. This alteration results from a G to A substitution at nucleotide position 518, causing the arginine (R) at amino acid position 173 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