rs2723142
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000421563.5(LINC02923):n.222+91C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,200 control chromosomes in the GnomAD database, including 552 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 0.087 ( 552 hom., cov: 32)
Exomes 𝑓: 0.071 ( 0 hom. )
Consequence
LINC02923
ENST00000421563.5 intron
ENST00000421563.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.308
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC02923 | NR_187213.1 | n.6241+91C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02923 | ENST00000421563.5 | n.222+91C>T | intron_variant | 4 | ||||||
LINC02923 | ENST00000430051.1 | n.296+91C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0865 AC: 13151AN: 152068Hom.: 550 Cov.: 32
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GnomAD4 exome AF: 0.0714 AC: 1AN: 14Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 10
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GnomAD4 genome AF: 0.0865 AC: 13165AN: 152186Hom.: 552 Cov.: 32 AF XY: 0.0865 AC XY: 6437AN XY: 74390
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at