rs11260603
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_038869.1(LINC01342):n.1382T>C 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 0.332 in 151,972 control chromosomes in the GnomAD database, including 10,135 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 0.33 ( 10126 hom., cov: 33)
Exomes 𝑓: 0.24 ( 9 hom. )
Consequence
LINC01342
NR_038869.1 non_coding_transcript_exon
NR_038869.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.69
Genes affected
LINC01342 (HGNC:50551): (long intergenic non-protein coding RNA 1342)
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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=-1.01).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01342 | NR_038869.1 | n.1382T>C | non_coding_transcript_exon_variant | 3/3 | |||
LOC124903820 | XR_007065351.1 | n.76-14664T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01342 | ENST00000416774.1 | n.1382T>C | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.332 AC: 50334AN: 151620Hom.: 10095 Cov.: 33
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GnomAD4 exome AF: 0.237 AC: 56AN: 236Hom.: 9 Cov.: 0 AF XY: 0.247 AC XY: 46AN XY: 186
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GnomAD4 genome ? AF: 0.332 AC: 50413AN: 151736Hom.: 10126 Cov.: 33 AF XY: 0.331 AC XY: 24582AN XY: 74166
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at