ENST00000539078.1:n.167+20G>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000539078.1(PUS1-AS1):n.167+20G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 150,912 control chromosomes in the GnomAD database, including 2,464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000539078.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PUS1 | NM_025215.6 | c.-558C>G | upstream_gene_variant | ENST00000376649.8 | NP_079491.2 | |||
PUS1 | NM_001002019.3 | c.-250C>G | upstream_gene_variant | NP_001002019.1 | ||||
PUS1 | NM_001002020.3 | c.-226C>G | upstream_gene_variant | NP_001002020.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.164 AC: 24718AN: 150654Hom.: 2461 Cov.: 26
GnomAD4 exome AF: 0.00685 AC: 1AN: 146Hom.: 0 Cov.: 0 AF XY: 0.00980 AC XY: 1AN XY: 102
GnomAD4 genome AF: 0.164 AC: 24736AN: 150766Hom.: 2464 Cov.: 26 AF XY: 0.164 AC XY: 12103AN XY: 73646
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at