13-30630894-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001321532.2(USPL1):c.-256A>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000197 in 1,613,812 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 Likely benign (★).
Frequency
Consequence
NM_001321532.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USPL1 | ENST00000255304.9 | c.288A>C | p.Glu96Asp | missense_variant | Exon 4 of 9 | 1 | NM_005800.5 | ENSP00000255304.4 | ||
USPL1 | ENST00000614860.1 | c.-119-6850A>C | intron_variant | Intron 2 of 6 | 1 | ENSP00000480656.1 | ||||
USPL1 | ENST00000465952.5 | n.553A>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 250986Hom.: 1 AF XY: 0.000155 AC XY: 21AN XY: 135660
GnomAD4 exome AF: 0.000194 AC: 283AN: 1461594Hom.: 1 Cov.: 31 AF XY: 0.000188 AC XY: 137AN XY: 727114
GnomAD4 genome AF: 0.000230 AC: 35AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at