X-14796872-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001410764.1(FANCB):c.2654G>A(p.Trp885*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 110,081 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., 1 hem., cov: 21)
Consequence
FANCB
NM_001410764.1 stop_gained
NM_001410764.1 stop_gained
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.659
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 Uncertain_significance. Variant got 4 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0487 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FANCB | NM_001410764.1 | c.2654G>A | p.Trp885* | stop_gained | Exon 12 of 13 | NP_001397693.1 | ||
| FANCB | XR_001755672.2 | n.2929G>A | non_coding_transcript_exon_variant | Exon 12 of 15 | ||||
| FANCB | XR_001755673.2 | n.6871G>A | non_coding_transcript_exon_variant | Exon 11 of 14 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FANCB | ENST00000696353.1 | c.2654G>A | p.Trp885* | stop_gained | Exon 12 of 13 | ENSP00000512574.1 | ||||
| FANCB | ENST00000696354 | c.*271G>A | 3_prime_UTR_variant | Exon 11 of 11 | ENSP00000512575.1 | |||||
| FANCB | ENST00000696322.1 | n.*1659G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | ENSP00000512559.1 |
Frequencies
GnomAD3 genomes 0.0000273 AC: 3AN: 110081Hom.: 0 Cov.: 21 AF XY: 0.0000309 AC XY: 1AN XY: 32311
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000273 AC: 3AN: 110081Hom.: 0 Cov.: 21 AF XY: 0.0000309 AC XY: 1AN XY: 32311
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
FANCB: PVS1:Moderate -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at