rs1122341
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183740.1(LINC02030):n.483+13832T>C 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 0.154 in 152,146 control chromosomes in the GnomAD database, including 2,485 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 ( 2485 hom., cov: 32)
Consequence
LINC02030
NR_183740.1 intron, non_coding_transcript
NR_183740.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.308
Genes affected
LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02030 | NR_183740.1 | n.483+13832T>C | intron_variant, non_coding_transcript_variant | ||||
LOC124906243 | XR_007095917.1 | n.158+6468A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02030 | ENST00000654581.1 | n.363-25924T>C | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000662390.1 | n.321-25924T>C | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000670191.1 | n.212+13832T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.154 AC: 23423AN: 152028Hom.: 2476 Cov.: 32
GnomAD3 genomes
?
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23423
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152028
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.154 AC: 23442AN: 152146Hom.: 2485 Cov.: 32 AF XY: 0.155 AC XY: 11561AN XY: 74368
GnomAD4 genome
?
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AC:
23442
AN:
152146
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Cov.:
32
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11561
AN XY:
74368
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522
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3478
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