11-78196420-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020798.4(USP35):c.175C>T(p.Arg59Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000371 in 1,294,522 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020798.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
USP35 | ENST00000529308.6 | c.175C>T | p.Arg59Cys | missense_variant | Exon 2 of 11 | 5 | NM_020798.4 | ENSP00000431876.1 | ||
USP35 | ENST00000528910.5 | c.-59-1516C>T | intron_variant | Intron 1 of 8 | 1 | ENSP00000436001.1 | ||||
USP35 | ENST00000530267.5 | c.-100+7263C>T | intron_variant | Intron 1 of 5 | 2 | ENSP00000435468.1 | ||||
USP35 | ENST00000530535.5 | n.335+7263C>T | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000200 AC: 30AN: 150042Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000189 AC: 2AN: 10588Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 6720
GnomAD4 exome AF: 0.0000157 AC: 18AN: 1144480Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 7AN XY: 556672
GnomAD4 genome AF: 0.000200 AC: 30AN: 150042Hom.: 1 Cov.: 32 AF XY: 0.000178 AC XY: 13AN XY: 73234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.175C>T (p.R59C) alteration is located in exon 2 (coding exon 1) of the USP35 gene. This alteration results from a C to T substitution at nucleotide position 175, causing the arginine (R) at amino acid position 59 to be replaced by a cysteine (C). 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