rs13047060
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024089.2(PICSAR):n.136C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,148 control chromosomes in the GnomAD database, including 16,541 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.43 ( 16522 hom., cov: 32)
Exomes 𝑓: 0.44 ( 19 hom. )
Consequence
PICSAR
NR_024089.2 non_coding_transcript_exon
NR_024089.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.41
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PICSAR | NR_024089.2 | n.136C>A | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PICSAR | ENST00000615826.1 | n.136C>A | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.431 AC: 65522AN: 151898Hom.: 16515 Cov.: 32
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GnomAD4 exome AF: 0.439 AC: 58AN: 132Hom.: 19 Cov.: 0 AF XY: 0.404 AC XY: 38AN XY: 94
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GnomAD4 genome ? AF: 0.431 AC: 65554AN: 152016Hom.: 16522 Cov.: 32 AF XY: 0.441 AC XY: 32756AN XY: 74286
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at