16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGTGTGTGTGT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NR_103859.1(LINC01082):n.232+1357_232+1362dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.015 ( 36 hom., cov: 0)
Consequence
LINC01082
NR_103859.1 intron, non_coding_transcript
NR_103859.1 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.11
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0149 (2198/147954) while in subpopulation AFR AF= 0.0329 (1306/39738). AF 95% confidence interval is 0.0314. There are 36 homozygotes in gnomad4. There are 1225 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 36 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01082 | NR_103859.1 | n.232+1357_232+1362dup | intron_variant, non_coding_transcript_variant | ||||
LOC124903743 | XR_007065164.1 | n.628-566_628-565insACACAC | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000599841.1 | n.25-566_25-565insACACAC | intron_variant, non_coding_transcript_variant | 4 | ||||||
LINC01082 | ENST00000669926.2 | n.459+1357_459+1362dup | intron_variant, non_coding_transcript_variant | ||||||
LINC01082 | ENST00000601250.1 | n.232+1357_232+1362dup | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2197AN: 147848Hom.: 36 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0149 AC: 2198AN: 147954Hom.: 36 Cov.: 0 AF XY: 0.0170 AC XY: 1225AN XY: 71978
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at