rs17077348
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000507361.5(LINC01411):n.223+2851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,134 control chromosomes in the GnomAD database, including 188 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 0.045 ( 188 hom., cov: 32)
Consequence
LINC01411
ENST00000507361.5 intron
ENST00000507361.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.949
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.083 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC01411 | NR_125806.1 | n.223+2851G>A | intron_variant | Intron 1 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC01411 | ENST00000507361.5 | n.223+2851G>A | intron_variant | Intron 1 of 3 | 3 | |||||
LINC01411 | ENST00000510234.5 | n.82+2851G>A | intron_variant | Intron 1 of 5 | 3 | |||||
LINC01411 | ENST00000515513.5 | n.282+2851G>A | intron_variant | Intron 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0446 AC: 6777AN: 152016Hom.: 188 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: 0.0446 AC: 6782AN: 152134Hom.: 188 Cov.: 32 AF XY: 0.0433 AC XY: 3223AN XY: 74382
GnomAD4 genome
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32
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74382
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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