rs5004866
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The XR_931202.2(LOC105376634):n.555-56352A>T 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 0.48 ( 405 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
LOC105376634
XR_931202.2 intron, non_coding_transcript
XR_931202.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0210
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=-1.05).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105376634 | XR_931202.2 | n.555-56352A>T | 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: 0.00 AC: 8494AN: 17698Hom.: 405 Cov.: 0 FAILED QC
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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: 0.480 AC: 8511AN: 17742Hom.: 405 Cov.: 0 AF XY: 0.481 AC XY: 4348AN XY: 9042
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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8511
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17742
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0
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4348
AN XY:
9042
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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