rs7103674
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2
The NM_022725.4(FANCF):c.624G>T(p.Ala208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,610,804 control chromosomes in the GnomAD database, including 55 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 31 hom., cov: 33)
Exomes 𝑓: 0.00098 ( 24 hom. )
Consequence
FANCF
NM_022725.4 synonymous
NM_022725.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.0290
Genes affected
FANCF (HGNC:3587): (FA complementation group F) The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group F. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP6
?
Variant 11-22625187-C-A is Benign according to our data. Variant chr11-22625187-C-A is described in ClinVar as [Benign]. Clinvar id is 241442.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.029 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00967 (1472/152300) while in subpopulation AFR AF= 0.0338 (1404/41556). AF 95% confidence interval is 0.0323. There are 31 homozygotes in gnomad4. There are 692 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 31 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCF | NM_022725.4 | c.624G>T | p.Ala208= | synonymous_variant | 1/1 | ENST00000327470.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCF | ENST00000327470.6 | c.624G>T | p.Ala208= | synonymous_variant | 1/1 | NM_022725.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00967 AC: 1472AN: 152182Hom.: 31 Cov.: 33
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GnomAD3 exomes AF: 0.00265 AC: 658AN: 248206Hom.: 12 AF XY: 0.00198 AC XY: 266AN XY: 134590
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GnomAD4 exome AF: 0.000979 AC: 1428AN: 1458504Hom.: 24 Cov.: 32 AF XY: 0.000860 AC XY: 624AN XY: 725300
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GnomAD4 genome ? AF: 0.00967 AC: 1472AN: 152300Hom.: 31 Cov.: 33 AF XY: 0.00929 AC XY: 692AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fanconi anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at