chrX-14782377-T-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000696352.1(FANCB):c.*107+13783A>G variant causes a intron, NMD 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 0.62 ( 15858 hom., 19826 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
FANCB
ENST00000696352.1 intron, NMD_transcript
ENST00000696352.1 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.474
Genes affected
FANCB (HGNC:3583): (FA complementation group B) This gene encodes a member of the Fanconi anemia complementation group B. This protein is assembled into a nucleoprotein complex that is involved in the repair of DNA lesions. Mutations in this gene can cause chromosome instability and VACTERL syndrome with hydrocephalus. [provided by RefSeq, Apr 2016]
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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=-1.01).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCB | XR_001755672.2 | n.3172+13783A>G | intron_variant, non_coding_transcript_variant | ||||
FANCB | XR_001755673.2 | n.7114+13783A>G | intron_variant, non_coding_transcript_variant | ||||
FANCB | XR_001755674.2 | n.3051+13783A>G | intron_variant, non_coding_transcript_variant | ||||
FANCB | XR_007068184.1 | n.3151+13783A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCB | ENST00000696351.1 | c.*514+13783A>G | intron_variant, NMD_transcript_variant | ||||||
FANCB | ENST00000696352.1 | c.*107+13783A>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.623 AC: 68700AN: 110230Hom.: 15864 Cov.: 22 AF XY: 0.609 AC XY: 19781AN XY: 32470
GnomAD3 genomes
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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: 0.623 AC: 68730AN: 110280Hom.: 15858 Cov.: 22 AF XY: 0.609 AC XY: 19826AN XY: 32530
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