11-78196720-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.475C>T(p.Pro159Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000145 in 1,378,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP35 | NM_020798.4 | c.475C>T | p.Pro159Ser | missense_variant | 2/11 | ENST00000529308.6 | NP_065849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP35 | ENST00000529308.6 | c.475C>T | p.Pro159Ser | missense_variant | 2/11 | 5 | NM_020798.4 | ENSP00000431876 | P1 | |
USP35 | ENST00000528910.5 | c.-59-1216C>T | intron_variant | 1 | ENSP00000436001 | |||||
USP35 | ENST00000530267.5 | c.-100+7563C>T | intron_variant | 2 | ENSP00000435468 | |||||
USP35 | ENST00000530535.5 | n.335+7563C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1378252Hom.: 0 Cov.: 31 AF XY: 0.00000147 AC XY: 1AN XY: 680060
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.475C>T (p.P159S) 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 475, causing the proline (P) at amino acid position 159 to be replaced by a serine (S). 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