rs279612
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183453.1(LINC02855):n.198+1943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,268 control chromosomes in the GnomAD database, including 399 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 0.059 ( 399 hom., cov: 32)
Consequence
LINC02855
NR_183453.1 intron
NR_183453.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.222
Genes affected
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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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC02855 | NR_183453.1 | n.198+1943T>C | intron_variant | |||||
LINC02855 | NR_183454.1 | n.198+1943T>C | intron_variant | |||||
LINC02855 | NR_183455.1 | n.47+3460T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAS2-AS1 | ENST00000458107.3 | n.252-13493A>G | intron_variant | 5 | ||||||
HAS2-AS1 | ENST00000648171.1 | n.753-13493A>G | intron_variant | |||||||
HAS2-AS1 | ENST00000663147.1 | n.729-13493A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0595 AC: 9054AN: 152150Hom.: 399 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0594 AC: 9052AN: 152268Hom.: 399 Cov.: 32 AF XY: 0.0598 AC XY: 4454AN XY: 74452
GnomAD4 genome
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207
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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