rs757444090
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032172.3(USP42):c.1262T>A(p.Leu421His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,594,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032172.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000456 AC: 11AN: 241184 AF XY: 0.0000688 show subpopulations
GnomAD4 exome AF: 0.0000166 AC: 24AN: 1442012Hom.: 0 Cov.: 30 AF XY: 0.0000266 AC XY: 19AN XY: 713982 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1262T>A (p.L421H) alteration is located in exon 12 (coding exon 11) of the USP42 gene. This alteration results from a T to A substitution at nucleotide position 1262, causing the leucine (L) at amino acid position 421 to be replaced by a histidine (H). 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