rs544395896
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_022725.4(FANCF):c.90C>T(p.Thr30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,164 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. T30T) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCF | NM_022725.4 | c.90C>T | p.Thr30= | synonymous_variant | 1/1 | ENST00000327470.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCF | ENST00000327470.6 | c.90C>T | p.Thr30= | synonymous_variant | 1/1 | NM_022725.4 | P1 | ||
GAS2 | ENST00000528582.5 | c.-113G>A | 5_prime_UTR_variant | 1/6 | 3 | ||||
GAS2 | ENST00000648096.1 | n.213G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250290Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135602
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461800Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727210
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74506
ClinVar
Submissions by phenotype
Fanconi anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 2019 | - - |
FANCF-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 13, 2023 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at