4-143186094-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032557.6(USP38):c.644C>T(p.Pro215Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,036 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.644C>T | p.Pro215Leu | missense_variant | Exon 1 of 10 | ENST00000307017.9 | NP_115946.2 | |
USP38 | NM_001410848.1 | c.644C>T | p.Pro215Leu | missense_variant | Exon 1 of 9 | NP_001397777.1 | ||
USP38 | NM_001290325.1 | c.644C>T | p.Pro215Leu | missense_variant | Exon 1 of 9 | NP_001277254.1 | ||
USP38 | NM_001290326.1 | c.-838C>T | 5_prime_UTR_variant | Exon 1 of 11 | NP_001277255.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727228
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.644C>T (p.P215L) alteration is located in exon 1 (coding exon 1) of the USP38 gene. This alteration results from a C to T substitution at nucleotide position 644, causing the proline (P) at amino acid position 215 to be replaced by a leucine (L). 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