rs201436396
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001018113.3(FANCB):c.2477C>T(p.Thr826Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,207,512 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 121 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001018113.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.2477C>T | p.Thr826Met | missense_variant | Exon 10 of 10 | ENST00000650831.1 | NP_001018123.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000314 AC: 35AN: 111488Hom.: 0 Cov.: 23 AF XY: 0.000297 AC XY: 10AN XY: 33704
GnomAD3 exomes AF: 0.000334 AC: 61AN: 182654Hom.: 0 AF XY: 0.000312 AC XY: 21AN XY: 67300
GnomAD4 exome AF: 0.000307 AC: 336AN: 1096024Hom.: 0 Cov.: 29 AF XY: 0.000307 AC XY: 111AN XY: 361444
GnomAD4 genome AF: 0.000314 AC: 35AN: 111488Hom.: 0 Cov.: 23 AF XY: 0.000297 AC XY: 10AN XY: 33704
ClinVar
Submissions by phenotype
Fanconi anemia complementation group B Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Fanconi anemia Benign:2
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FANCB-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
FANCB: BP4, BS2 -
VACTERL association, X-linked, with or without hydrocephalus Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at