chr11-22625553-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_022725.4(FANCF):c.258C>T(p.Leu86=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L86L) has been classified as Likely benign.
Frequency
Consequence
NM_022725.4 synonymous
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCF | NM_022725.4 | c.258C>T | p.Leu86= | synonymous_variant | 1/1 | ENST00000327470.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCF | ENST00000327470.6 | c.258C>T | p.Leu86= | synonymous_variant | 1/1 | NM_022725.4 | P1 | ||
GAS2 | ENST00000648096.1 | n.45G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250582Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135726
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461754Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727182
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74384
ClinVar
Submissions by phenotype
Fanconi anemia Benign:2
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Dec 23, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at