X-47233066-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001371072.1(USP11):c.23C>T(p.Pro8Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,208,049 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001371072.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP11 | NM_001371072.1 | c.23C>T | p.Pro8Leu | missense_variant | Exon 1 of 21 | ENST00000377107.7 | NP_001358001.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP11 | ENST00000377107.7 | c.23C>T | p.Pro8Leu | missense_variant | Exon 1 of 21 | 1 | NM_001371072.1 | ENSP00000366311.2 | ||
USP11 | ENST00000218348.7 | c.152C>T | p.Pro51Leu | missense_variant | Exon 1 of 21 | 1 | ENSP00000218348.3 | |||
USP11 | ENST00000469080.5 | n.37C>T | non_coding_transcript_exon_variant | Exon 1 of 19 | 1 | |||||
USP11 | ENST00000478596.5 | n.83C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112531Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34663
GnomAD3 exomes AF: 0.0000935 AC: 16AN: 171109Hom.: 0 AF XY: 0.0000838 AC XY: 5AN XY: 59695
GnomAD4 exome AF: 0.0000110 AC: 12AN: 1095518Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 4AN XY: 361220
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112531Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34663
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.152C>T (p.P51L) alteration is located in exon 1 (coding exon 1) of the USP11 gene. This alteration results from a C to T substitution at nucleotide position 152, causing the proline (P) at amino acid position 51 to be replaced by a leucine (L). 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