rs12664111
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_038399.2(FILNC1):n.52-38086A>G 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 0.0989 in 152,228 control chromosomes in the GnomAD database, including 1,095 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 0.099 ( 1095 hom., cov: 32)
Consequence
FILNC1
NR_038399.2 intron, non_coding_transcript
NR_038399.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00200
Genes affected
FILNC1 (HGNC:53755): (FOXO induced long non-coding RNA 1) This gene produces a long non-coding RNA that is induced by forkhead box O proteins and plays a role in stress-induced apoptosis. Knock down of transcripts at this locus results in increased renal tumor growth and alteration in genes involved in glucose metabolism. This RNA interacts with heterogeneous nuclear ribonucleoprotein D and prevents it from binding to Myc mRNA, therefore suppressing Myc activity. Alternative splicing and transcriptional start site usage results in multiple transcript variants. [provided by RefSeq, Oct 2017]
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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 (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FILNC1 | NR_038399.2 | n.52-38086A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FILNC1 | ENST00000647189.1 | n.255-38086A>G | intron_variant, non_coding_transcript_variant | ||||||
FILNC1 | ENST00000642381.1 | n.252-38086A>G | intron_variant, non_coding_transcript_variant | ||||||
FILNC1 | ENST00000644936.1 | n.204-38086A>G | intron_variant, non_coding_transcript_variant | ||||||
FILNC1 | ENST00000647420.1 | n.208-38086A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0989 AC: 15038AN: 152110Hom.: 1088 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: 0.0989 AC: 15060AN: 152228Hom.: 1095 Cov.: 32 AF XY: 0.101 AC XY: 7520AN XY: 74436
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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