17-9645756-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153210.5(USP43):c.124G>A(p.Gly42Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000241 in 1,244,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153210.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP43 | ENST00000285199.12 | c.124G>A | p.Gly42Arg | missense_variant | Exon 1 of 15 | 1 | NM_153210.5 | ENSP00000285199.6 | ||
USP43 | ENST00000570475.5 | c.124G>A | p.Gly42Arg | missense_variant | Exon 1 of 15 | 1 | ENSP00000458963.1 | |||
USP43 | ENST00000570827.6 | n.645+414G>A | intron_variant | Intron 1 of 14 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000288 AC: 1AN: 34694Hom.: 0 AF XY: 0.0000478 AC XY: 1AN XY: 20934
GnomAD4 exome AF: 0.00000241 AC: 3AN: 1244960Hom.: 0 Cov.: 30 AF XY: 0.00000492 AC XY: 3AN XY: 609872
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124G>A (p.G42R) alteration is located in exon 1 (coding exon 1) of the USP43 gene. This alteration results from a G to A substitution at nucleotide position 124, causing the glycine (G) at amino acid position 42 to be replaced by an arginine (R). 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