rs1368374192
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The ENST00000289081.8(FANCC):c.3G>T(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.000000684 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FANCC
ENST00000289081.8 start_lost
ENST00000289081.8 start_lost
Scores
8
6
2
Clinical Significance
Conservation
PhyloP100: 5.31
Genes affected
FANCC (HGNC:3584): (FA complementation group C) 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 C. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Start lost variant, no new inframe start found.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-95249289-C-A is Pathogenic according to our data. Variant chr9-95249289-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 557034.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCC | NM_000136.3 | c.3G>T | p.Met1? | start_lost | 2/15 | ENST00000289081.8 | NP_000127.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FANCC | ENST00000289081.8 | c.3G>T | p.Met1? | start_lost | 2/15 | 1 | NM_000136.3 | ENSP00000289081 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250170Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135324
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461770Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727192
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Fanconi anemia complementation group C Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 07, 2018 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The p.M1? pathogenic mutation (also known as c.3G>T) is located in coding exon 1 of the FANCC gene and results from a G to T substitution at nucleotide position 3. This alters the methionine residue at the initiation codon (ATG). Although there is an alternate in-frame methionine 16 amino acids downstream from the initiation site, alterations truncating the protein between p.M1 and p.M16 are identified in many patients with Fanconi Anemia (Chandrasekharappa SC et al. Blood, 2013 May;121:e138-48; Steinberg-Shemer O et al. Haematologica, 2020 07;105:1825-1834; Murer-Orlando M et al. Lancet, 1993 Sep;342:686; Verlander PC et al. Am J Hum Genet, 1994 Apr;54:595-601; Gillio AP et al. Blood, 1997 Jul;90:105-10; Nicchia E et al. Mol Genet Genomic Med, 2015 Nov;3:500-12). In addition to the clinical data presented in the literature, sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;D;T;.;T;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PROVEAN
Uncertain
D;D;.;.;D;.;.;.
REVEL
Uncertain
Sift
Pathogenic
D;D;.;.;D;.;.;.
Sift4G
Pathogenic
D;D;D;.;D;.;.;.
Polyphen
D;D;.;.;D;.;.;.
Vest4
MutPred
Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);Gain of catalytic residue at M1 (P = 0.0409);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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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