rs7892812
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The XR_001755783.2(LOC107985675):n.6225+886A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.59 ( 14363 hom., 18260 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
LOC107985675
XR_001755783.2 intron, non_coding_transcript
XR_001755783.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.502
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107985675 | XR_001755783.2 | n.6225+886A>G | intron_variant, non_coding_transcript_variant | ||||
LOC107985675 | XR_001755782.2 | n.1986-13616A>G | intron_variant, non_coding_transcript_variant | ||||
LOC107985675 | XR_001755784.2 | n.1986-13616A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.595 AC: 64807AN: 108972Hom.: 14364 Cov.: 21 AF XY: 0.582 AC XY: 18205AN XY: 31306
GnomAD3 genomes
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21
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31306
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.595 AC: 64860AN: 109031Hom.: 14363 Cov.: 21 AF XY: 0.582 AC XY: 18260AN XY: 31373
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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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