1-161161073-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001014443.3(USP21):c.433C>T(p.Arg145Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 1,614,250 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R145Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001014443.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP21 | ENST00000368002.8 | c.433C>T | p.Arg145Trp | missense_variant | Exon 3 of 14 | 1 | NM_001014443.3 | ENSP00000356981.3 | ||
USP21 | ENST00000289865.12 | c.433C>T | p.Arg145Trp | missense_variant | Exon 2 of 13 | 1 | ENSP00000289865.8 | |||
USP21 | ENST00000368001.1 | c.433C>T | p.Arg145Trp | missense_variant | Exon 2 of 13 | 1 | ENSP00000356980.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251328Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135850
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461890Hom.: 2 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 727246
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.433C>T (p.R145W) alteration is located in exon 3 (coding exon 1) of the USP21 gene. This alteration results from a C to T substitution at nucleotide position 433, causing the arginine (R) at amino acid position 145 to be replaced by a tryptophan (W). 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