12-109052752-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032663.5(USP30):c.74C>A(p.Ala25Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,454,246 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032663.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP30 | NM_032663.5 | c.74C>A | p.Ala25Glu | missense_variant | 1/13 | ENST00000257548.10 | |
USP30-AS1 | NR_038996.1 | n.281-14G>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP30 | ENST00000257548.10 | c.74C>A | p.Ala25Glu | missense_variant | 1/13 | 1 | NM_032663.5 | P2 | |
USP30-AS1 | ENST00000478808.4 | n.302-14G>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000118 AC: 13AN: 109762Hom.: 0 AF XY: 0.000143 AC XY: 9AN XY: 62820
GnomAD4 exome AF: 0.000154 AC: 200AN: 1302046Hom.: 2 Cov.: 32 AF XY: 0.000142 AC XY: 91AN XY: 639500
GnomAD4 genome AF: 0.000118 AC: 18AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.74C>A (p.A25E) alteration is located in exon 1 (coding exon 1) of the USP30 gene. This alteration results from a C to A substitution at nucleotide position 74, causing the alanine (A) at amino acid position 25 to be replaced by a glutamic acid (E). 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