rs1978503
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000654280.1(LINC01416):n.1169T>C 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 0.181 in 152,112 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 0.18 ( 2580 hom., cov: 32)
Consequence
LINC01416
ENST00000654280.1 non_coding_transcript_exon
ENST00000654280.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.381
Genes affected
LINC01416 (HGNC:51645): (long intergenic non-protein coding RNA 1416)
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC03092 | XR_001753454.2 | n.841A>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01416 | ENST00000654280.1 | n.1169T>C | non_coding_transcript_exon_variant | 1/4 | |||||
LINC03092 | ENST00000589440.1 | n.406-20677A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
LINC01416 | ENST00000655696.1 | n.960T>C | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27507AN: 151994Hom.: 2572 Cov.: 32
GnomAD3 genomes
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151994
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.181 AC: 27546AN: 152112Hom.: 2580 Cov.: 32 AF XY: 0.178 AC XY: 13201AN XY: 74364
GnomAD4 genome
?
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27546
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152112
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32
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13201
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74364
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549
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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