rs2099378
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_187367.1(LINC02715):n.420-4809A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,046 control chromosomes in the GnomAD database, including 16,854 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 0.39 ( 16854 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
LINC02715
NR_187367.1 intron
NR_187367.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.206
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC02715 | NR_187367.1 | n.420-4809A>G | intron_variant | |||||
LINC02715 | NR_187368.1 | n.284-4809A>G | intron_variant | |||||
LINC02715 | NR_187369.1 | n.475-4809A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02715 | ENST00000662064.1 | n.304-4809A>G | intron_variant | |||||||
LINC02715 | ENST00000667432.1 | n.414-4809A>G | intron_variant | |||||||
LINC02715 | ENST00000534252.2 | n.*14A>G | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.395 AC: 59943AN: 151924Hom.: 16809 Cov.: 32
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32
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome AF: 0.395 AC: 60048AN: 152044Hom.: 16854 Cov.: 32 AF XY: 0.386 AC XY: 28713AN XY: 74328
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at