chrX-14844672-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001018113.3(FANCB):c.1996G>A(p.Gly666Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00084 in 1,208,885 control chromosomes in the GnomAD database, including 7 homozygotes. There are 276 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001018113.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.1996G>A | p.Gly666Ser | missense_variant | Exon 9 of 10 | ENST00000650831.1 | NP_001018123.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 347AN: 111473Hom.: 1 Cov.: 23 AF XY: 0.00291 AC XY: 98AN XY: 33725
GnomAD3 exomes AF: 0.00116 AC: 212AN: 183142Hom.: 0 AF XY: 0.000856 AC XY: 58AN XY: 67780
GnomAD4 exome AF: 0.000604 AC: 663AN: 1097362Hom.: 6 Cov.: 30 AF XY: 0.000477 AC XY: 173AN XY: 362772
GnomAD4 genome AF: 0.00317 AC: 353AN: 111523Hom.: 1 Cov.: 23 AF XY: 0.00305 AC XY: 103AN XY: 33785
ClinVar
Submissions by phenotype
not specified Benign:2
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History of neurodevelopmental disorder Uncertain:1
Co-segregation data for this variant is currently unavailable.This variant has not been detected in conjunction with a pathogenic mutation to date.This variant was previously reported in the SNPDatabase as rs145110602. Based on data from the NHLBI Exome Sequencing Project (ESP), the A-allele has an overall frequency of approximately 0.25% (5/1997) total male alleles studied and but was not observed in the homozygous state out of 3381females studied. The A-allele was observed in 0.96% (5/522) African American male alleles but was absent out of 1475 European American male alleles studied. Based on data from the 1000 Genomes Project, the A-allele has an overall frequency of approximately 2/1048 (0.19%) and the highest frequency was in 2/48 (4.17%) African-American SW male chromosomes studied.This amino acid position is not conserved on species alignment.This alteration is predicted to be benign with a score of 0.002 (sensitivity: 0.99; specificity: 0.17)This alteration is predicted to be tolerated with a score of 0.390 (conservation: 2.57) -
Fanconi anemia complementation group B Benign:1
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Fanconi anemia Benign:1
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FANCB-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at