10-28801677-G-A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000426922.6(LINC01517):n.290-110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,176 control chromosomes in the GnomAD database, including 17,448 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
Consequence
ENST00000426922.6 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC01517 | NR_120652.1 | n.198-4370G>A | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC01517 | ENST00000426922.6 | n.290-110G>A | intron_variant | Intron 2 of 5 | 5 | |||||
LINC01517 | ENST00000616194.4 | n.425-110G>A | intron_variant | Intron 2 of 5 | 5 | |||||
LINC01517 | ENST00000621861.1 | n.631-4370G>A | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.441 AC: 67061AN: 151942Hom.: 17428 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.586 AC: 68AN: 116Hom.: 21 AF XY: 0.598 AC XY: 49AN XY: 82 show subpopulations
GnomAD4 genome AF: 0.441 AC: 67060AN: 152060Hom.: 17427 Cov.: 32 AF XY: 0.443 AC XY: 32894AN XY: 74294 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at