chr15-63574385-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006537.4(USP3):c.1078C>A(p.Pro360Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00442 in 1,603,716 control chromosomes in the GnomAD database, including 271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_006537.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0242 AC: 3680AN: 152070Hom.: 131 Cov.: 32
GnomAD3 exomes AF: 0.00581 AC: 1412AN: 243086Hom.: 46 AF XY: 0.00450 AC XY: 592AN XY: 131536
GnomAD4 exome AF: 0.00235 AC: 3409AN: 1451528Hom.: 140 Cov.: 30 AF XY: 0.00204 AC XY: 1470AN XY: 721790
GnomAD4 genome AF: 0.0242 AC: 3687AN: 152188Hom.: 131 Cov.: 32 AF XY: 0.0235 AC XY: 1749AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 19, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at