rs41309679
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001018113.3(FANCB):c.1004G>A(p.Gly335Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0731 in 1,187,007 control chromosomes in the GnomAD database, including 2,526 homozygotes. There are 27,854 hemizygotes in GnomAD. In-silico tool predicts 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.1004G>A | p.Gly335Glu | missense_variant | Exon 4 of 10 | ENST00000650831.1 | NP_001018123.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0546 AC: 6078AN: 111377Hom.: 156 Cov.: 23 AF XY: 0.0526 AC XY: 1769AN XY: 33625
GnomAD3 exomes AF: 0.0617 AC: 11246AN: 182122Hom.: 311 AF XY: 0.0656 AC XY: 4379AN XY: 66726
GnomAD4 exome AF: 0.0750 AC: 80647AN: 1075579Hom.: 2371 Cov.: 25 AF XY: 0.0758 AC XY: 26088AN XY: 344073
GnomAD4 genome AF: 0.0545 AC: 6072AN: 111428Hom.: 155 Cov.: 23 AF XY: 0.0524 AC XY: 1766AN XY: 33686
ClinVar
Submissions by phenotype
Fanconi anemia complementation group B Benign:4
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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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not specified Benign:2
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Fanconi anemia Benign:2
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not provided Benign:2
This variant is associated with the following publications: (PMID: 30679340) -
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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