rs3752596
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000458450.1(LINC01399):n.230C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 519,946 control chromosomes in the GnomAD database, including 141,895 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 0.62 ( 33720 hom., cov: 29)
Exomes 𝑓: 0.75 ( 108175 hom. )
Consequence
LINC01399
ENST00000458450.1 non_coding_transcript_exon
ENST00000458450.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.500
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=-0.7).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01399 | NR_126356.1 | n.222+144C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01399 | ENST00000458450.1 | n.230C>T | non_coding_transcript_exon_variant | 1/1 | |||||
LINC01399 | ENST00000423311.1 | n.222+144C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.616 AC: 93410AN: 151662Hom.: 33726 Cov.: 29
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GnomAD4 exome AF: 0.752 AC: 276985AN: 368166Hom.: 108175 Cov.: 2 AF XY: 0.758 AC XY: 149262AN XY: 196894
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GnomAD4 genome ? AF: 0.615 AC: 93415AN: 151780Hom.: 33720 Cov.: 29 AF XY: 0.617 AC XY: 45751AN XY: 74176
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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