X-14865123-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBS2_Supporting
The NM_001018113.3(FANCB):āc.388A>Gā(p.Met130Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,204,716 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M130L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001018113.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.388A>G | p.Met130Val | missense_variant | 3/10 | ENST00000650831.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCB | ENST00000650831.1 | c.388A>G | p.Met130Val | missense_variant | 3/10 | NM_001018113.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000446 AC: 5AN: 112226Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34390
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 177797Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63089
GnomAD4 exome AF: 0.00000824 AC: 9AN: 1092490Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 358616
GnomAD4 genome AF: 0.0000446 AC: 5AN: 112226Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34390
ClinVar
Submissions by phenotype
Fanconi anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at