rs10489087
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_121681.1(LINC01182):n.282-36988G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,928 control chromosomes in the GnomAD database, including 1,823 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 0.15 ( 1823 hom., cov: 33)
Consequence
LINC01182
NR_121681.1 intron, non_coding_transcript
NR_121681.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.877
Genes affected
LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01182 | NR_121681.1 | n.282-36988G>A | intron_variant, non_coding_transcript_variant | ||||
LOC101929048 | XR_925415.3 | n.303-5666C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01182 | ENST00000669061.1 | n.549-36988G>A | intron_variant, non_coding_transcript_variant | ||||||
ENST00000689499.2 | n.182-25832C>T | intron_variant, non_coding_transcript_variant | |||||||
LINC01182 | ENST00000510907.5 | n.282-36988G>A | intron_variant, non_coding_transcript_variant | 2 | |||||
ENST00000691923.2 | n.339-25832C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.147 AC: 22351AN: 151810Hom.: 1815 Cov.: 33
GnomAD3 genomes
?
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22351
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151810
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.147 AC: 22384AN: 151928Hom.: 1823 Cov.: 33 AF XY: 0.153 AC XY: 11348AN XY: 74274
GnomAD4 genome
?
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AC:
22384
AN:
151928
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33
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11348
AN XY:
74274
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658
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at