rs10490104
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_033873.1(LINC01122):n.4198G>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 0.0313 in 152,238 control chromosomes in the GnomAD database, including 248 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 0.031 ( 248 hom., cov: 32)
Exomes 𝑓: 0.33 ( 0 hom. )
Consequence
LINC01122
NR_033873.1 non_coding_transcript_exon
NR_033873.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.451
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01122 | NR_033873.1 | n.4198G>A | non_coding_transcript_exon_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01122 | ENST00000452840.5 | n.3979G>A | non_coding_transcript_exon_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0313 AC: 4767AN: 152114Hom.: 246 Cov.: 32
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GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2AN XY: 4
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GnomAD4 genome AF: 0.0313 AC: 4769AN: 152232Hom.: 248 Cov.: 32 AF XY: 0.0340 AC XY: 2531AN XY: 74428
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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