X-47233055-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001371072.1(USP11):c.12C>T(p.Val4Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,208,692 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001371072.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP11 | NM_001371072.1 | c.12C>T | p.Val4Val | synonymous_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.12C>T | p.Val4Val | synonymous_variant | Exon 1 of 21 | 1 | NM_001371072.1 | ENSP00000366311.2 | ||
USP11 | ENST00000218348.7 | c.141C>T | p.Val47Val | synonymous_variant | Exon 1 of 21 | 1 | ENSP00000218348.3 | |||
USP11 | ENST00000469080.5 | n.26C>T | non_coding_transcript_exon_variant | Exon 1 of 19 | 1 | |||||
USP11 | ENST00000478596.5 | n.72C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000445 AC: 5AN: 112364Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34520
GnomAD3 exomes AF: 0.0000288 AC: 5AN: 173648Hom.: 0 AF XY: 0.0000489 AC XY: 3AN XY: 61382
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1096328Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 4AN XY: 361862
GnomAD4 genome AF: 0.0000445 AC: 5AN: 112364Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34520
ClinVar
Submissions by phenotype
not provided Benign:1
USP11: BP4, BP7, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at