rs7858079
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109795.1(LINC01508):n.60-13847A>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 0.624 in 152,112 control chromosomes in the GnomAD database, including 30,548 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 ( 30548 hom., cov: 32)
Consequence
LINC01508
NR_109795.1 intron, non_coding_transcript
NR_109795.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.807
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=-1.02).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01508 | NR_109795.1 | n.60-13847A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01508 | ENST00000425666.2 | n.137-13847A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
LINC01508 | ENST00000436671.2 | n.76-11985A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
LINC01508 | ENST00000659218.1 | n.200-13847A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.625 AC: 94949AN: 151994Hom.: 30536 Cov.: 32
GnomAD3 genomes
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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: 0.624 AC: 94991AN: 152112Hom.: 30548 Cov.: 32 AF XY: 0.629 AC XY: 46812AN XY: 74378
GnomAD4 genome
?
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94991
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32
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46812
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74378
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2422
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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