rs505703
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_121681.1(LINC01182):n.350-9992C>T 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 0.199 in 152,060 control chromosomes in the GnomAD database, including 3,214 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 0.20 ( 3214 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: 0.178
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01182 | NR_121681.1 | n.350-9992C>T | intron_variant, non_coding_transcript_variant | ||||
LOC107986182 | XR_001741382.2 | n.3015-12186C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01182 | ENST00000669061.1 | n.713+80899C>T | intron_variant, non_coding_transcript_variant | ||||||
LINC01182 | ENST00000503532.1 | n.231-40631C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
LINC01182 | ENST00000510907.5 | n.350-9992C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30300AN: 151942Hom.: 3210 Cov.: 33
GnomAD3 genomes
?
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30300
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151942
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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: 0.199 AC: 30325AN: 152060Hom.: 3214 Cov.: 33 AF XY: 0.203 AC XY: 15052AN XY: 74298
GnomAD4 genome
?
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AC:
30325
AN:
152060
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33
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15052
AN XY:
74298
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688
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3476
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