rs73009150
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_174967.1(LINC02151):n.515G>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 0.0342 in 152,328 control chromosomes in the GnomAD database, including 119 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 0.034 ( 119 hom., cov: 33)
Exomes 𝑓: 0.10 ( 0 hom. )
Consequence
LINC02151
NR_174967.1 non_coding_transcript_exon
NR_174967.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.550
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=-0.87).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0341 (5200/152280) while in subpopulation NFE AF= 0.0501 (3404/67966). AF 95% confidence interval is 0.0487. There are 119 homozygotes in gnomad4. There are 2499 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 119 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02151 | NR_174967.1 | n.515G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02151 | ENST00000452629.2 | n.482G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0342 AC: 5200AN: 152162Hom.: 119 Cov.: 33
GnomAD3 genomes
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33
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GnomAD4 exome AF: 0.104 AC: 5AN: 48Hom.: 0 Cov.: 0 AF XY: 0.0333 AC XY: 1AN XY: 30
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GnomAD4 genome ? AF: 0.0341 AC: 5200AN: 152280Hom.: 119 Cov.: 33 AF XY: 0.0336 AC XY: 2499AN XY: 74484
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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