rs17023457
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NR_146623.1(LINC01780):n.82+4318T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.155 in 152,208 control chromosomes in the GnomAD database, including 2,580 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 ( 2580 hom., cov: 33)
Consequence
LINC01780
NR_146623.1 intron, non_coding_transcript
NR_146623.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.90
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.19).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01780 | NR_146623.1 | n.82+4318T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01780 | ENST00000457683.1 | n.82+4318T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.155 AC: 23533AN: 152090Hom.: 2581 Cov.: 33
GnomAD3 genomes
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23533
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.155 AC: 23530AN: 152208Hom.: 2580 Cov.: 33 AF XY: 0.159 AC XY: 11828AN XY: 74448
GnomAD4 genome
?
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23530
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33
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11828
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74448
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Asia WGS
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739
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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