rs4706205
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_132100.1(LINC01611):n.75T>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 0.49 in 151,838 control chromosomes in the GnomAD database, including 18,716 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 0.49 ( 18715 hom., cov: 32)
Exomes 𝑓: 0.75 ( 1 hom. )
Consequence
LINC01611
NR_132100.1 non_coding_transcript_exon
NR_132100.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.631
Genes affected
LINC01611 (HGNC:51791): (long intergenic non-protein coding RNA 1611)
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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=-1.02).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01611 | NR_132100.1 | n.75T>A | non_coding_transcript_exon_variant | 1/5 | |||
LOC107986620 | XR_001744235.2 | n.191+21528A>T | intron_variant, non_coding_transcript_variant | ||||
LOC107986620 | XR_001744236.1 | n.134+21528A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01611 | ENST00000454172.5 | n.135-30404T>A | intron_variant, non_coding_transcript_variant | 3 | |||||
LINC01611 | ENST00000428896.1 | n.75T>A | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.490 AC: 74295AN: 151716Hom.: 18704 Cov.: 32
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GnomAD4 exome AF: 0.750 AC: 3AN: 4Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3AN XY: 4
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GnomAD4 genome ? AF: 0.490 AC: 74343AN: 151834Hom.: 18715 Cov.: 32 AF XY: 0.491 AC XY: 36441AN XY: 74176
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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